Method and nucleic acids for the analysis of a colon cell proliferative disorder

ABSTRACT

The present invention relates to modified and genomic sequences, to oligonucleotides and/or PNA-oligomers for detecting the cytosine methylation state of genomic DNA, as well as to a method for ascertaining genetic and/or epigenetic parameters of genes for use in the differentiation, diagnosis, treatment and/or monitoring of colon cell proliferative disorders, or the predisposition to colon cell proliferative disorders.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation application of U.S. application Ser.No. 10/506,111, filed Sep. 16, 2005, now pending; which is a 35 USC §371National Stage application of International Application No.PCT/EP03/02035, filed Feb. 27, 2003, now expired; which claims thebenefit of priority to EP 02002551.4, filed Feb. 27, 2002, now expired.The disclosure of each of the prior applications is considered part of,and is incorporated by reference in, the disclosure of this application.

BACKGROUND OF THE INVENTION

1. Field of the Invention

Aspects of the invention relate generally to cellular proliferativedisorders (e.g., cancer) and genomic DNA methylation, and moreparticularly to modified and genomic sequences, to oligonucleotidesand/or PNA-oligomers for detecting the cytosine methylation state ofgenomic DNA, as well as to methods for ascertaining genetic and/orepigenetic parameters of genes for use in the differentiation,diagnosis, prognosis, treatment and/or monitoring of cellularproliferative disorders (e.g., cancer) including colon cellproliferative disorders, or the predisposition to colon cellproliferative disorders.

2. Background Information

The levels of observation that have been studied by the methodologicaldevelopments of recent years in molecular biology, are the genesthemselves, the translation of these genes into RNA, and the resultingproteins. The question of which gene is switched on at which point inthe course of the development of an individual, and how the activationand inhibition of specific genes in specific cells and tissues arecontrolled is correlatable to the degree and character of themethylation of the genes or of the genome. In this respect, pathogenicconditions may manifest themselves in a changed methylation pattern ofindividual genes or of the genome.

Colorectal cancer is the fourth leading cause of cancer mortality in menand women, although ranking third in frequency in men and second inwomen. The 5-year survival rate is 61% over all stages with earlydetection being a prerequisite for curative therapy of the disease. Upto 95% of all colorectal cancers are adenocarcinomas of varyingdifferentiation grades.

Sporadic colon cancer develops in a multistep process starting with thepathologic transformation of normal colonic epithelium to an adenomawhich consecutively progresses to invasive cancer. The progression rateof benign colonic adenomas depends strongly on their histologicappearance: whereas tubular-type adenomas tend to progress to malignanttumors very rarely, villous adenomas, particularly if larger than 2 cmin diameter, have a significant malignant potential.

During progression from benign proliferative lesions to malignantneoplasms several genetic and epigenetic alterations occur. Somaticmutation of the APC gene seems to be one of the earliest events in 75 to80% of colorectal adenomas and carcinomas. Activation of K-RAS isthought to be a critical step in the progression towards a malignantphenotype. Consecutively, mutations in other oncogenes as well asalterations leading to inactivation of tumour suppressor genesaccumulate.

Aberrant DNA methylation within CpG islands is among the earliest andmost common alterations in human malignancies leading to abrogation oroverexpression of a broad spectrum of genes. In addition, abnormalmethylation has been shown to occur in CpG rich regulatory elements inintronic and coding parts of genes for certain tumours. In contrast tothe specific hypermethylation of tumour suppressor genes, an overallhypomethylation of DNA can be observed in tumour cells. This decrease inglobal methylation can be detected early, far before the development offrank tumour formation. Also, correlation between hypomethylation andincreased gene expression was reported for many oncogenes. In coloncancer, aberrant DNA methylation constitutes one of the most prominentalterations and inactivates many tumor suppressor genes such as pl4ARF,pl6INK4a, THBS1, M3NT2, and M3NT31 and DNA mismatch repair genes such ashMLH1.

In the molecular evolution of colorectal cancer, DNA methylation errorshave been suggested to play two distinct roles. In normal colonic mucosacells, methylation errors accumulate as a function of age or astime-dependent events predisposing these cells to neoplastictransformation. For example, hypermethylation of several loci could beshown to be already present in adenomas, particularly in thetubulovillous and villous subtype. At later stages, increased DNAmethylation of CpG islands plays an important role in a subset oftumours affected by the so called CpG island methylator phenotype(CIMP). Most CIMP+ tumours, which constitute about 15% of all sporadiccolorectal cancers, are characterised by microsatellite instability(MIN) due to hypermethylation of the hMLH1 promoter and other DNAmismatch repair genes. By contrast, CIMP-colon cancers evolve along amore classic genetic instability pathway (CIN), with a high rate of p53mutations and chromosomal changes.

However, the molecular subtypes do not only show varying frequenciesregarding molecular alterations. According to the presence of eithermicro satellite instability or chromosomal aberrations, colon cancer canbe subclassified into two classes, which also exhibit significantclinical differences. Almost all MIN tumours originate in the proximalcolon (ascending and transversum), whereas 70% of CIN tumours arelocated in the distal colon and rectum. This has been attributed to thevarying prevalence of different carcinogens in different sections of thecolon. Methylating carcinogens, which constitute the prevailingcarcinogen in the proximal colon have been suggested to play a role inthe pathogenesis of MIN cancers, whereas CIN tumours are thought to bemore frequently caused by adduct-forming carcinogens, which occur morefrequently in distal parts of the colon and rectum. Moreover, MINtumours have a better prognosis than do tumours with a CIN phenotype andrespond better to adjuvant chemotherapy.

The identification of markers for the differentiation of colon carcinomaas well as for early detection are main goals of current research.

5-methylcytosine is the most frequent covalent base modification in theDNA of eukaryotic cells. It plays a role, for example, in the regulationof the transcription, in genetic imprinting, and in tumorigenesis.Therefore, the identification of 5-methylcytosine as a component ofgenetic information is of considerable interest. However,5-methylcytosine positions cannot be identified by sequencing since5-methylcytosine has the same base pairing behaviour as cytosine.Moreover, the epigenetic information carried by 5-methylcytosine iscompletely lost during PCR amplification.

A relatively new and currently the most frequently used method foranalysing DNA for 5-methylcytosine is based upon the specific reactionof bisulfite with cytosine which, upon subsequent alkaline hydrolysis,is converted to uracil which corresponds to thymidine in its basepairing behaviour. However, 5-methylcytosine remains unmodified underthese conditions. Consequently, the original DNA is converted in such amanner that methylcytosine, which originally could not be distinguishedfrom cytosine by its hybridisation behaviour, can now be detected as theonly remaining cytosine using “normal” molecular biological techniques,for example, by amplification and hybridisation or sequencing. All ofthese techniques are based on base pairing which can now be fullyexploited. In terms of sensitivity, the prior art is defined by a methodwhich encloses the DNA to be analysed in an agarose matrix, thuspreventing the diffusion and renaturation of the DNA (bisulfite onlyreacts with single-stranded DNA), and which replaces all precipitationand purification steps with fast dialysis (Olek A, Oswald J, Walter J. Amodified and improved method for bisulphite based cytosine methylationanalysis. Nucleic Acids Res. 1996 Dec. 15; 24(24):5064-6). Using thismethod, it is possible to analyse individual cells, which illustratesthe potential of the method. However, currently only individual regionsof a length of up to approximately 3000 base pairs are analysed, aglobal analysis of cells for thousands of possible methylation events isnot possible. However, this method cannot reliably analyse very smallfragments from small sample quantities either. These are lost throughthe matrix in spite of the diffusion protection.

An overview of the further known methods of detecting 5-methylcytosinemay be gathered from the following review article: Rein, T.,DePamphilis, M. L., Zorbas, H., Nucleic Acids Res. 1998, 26, 2255.

To date, barring few exceptions (e.g., Zeschnigk M, Lich C, Buiting K,Doerfler W. Horsthemke B. A single-tube PCR test for the diagnosis ofAngelman and Prader-Willi syndrome based on allelic methylationdifferences at the SNRPN locus. Eur J Hum Genet. 1997 March-April;5(2):94-8) the bisulfite technique is only used in research. Always,however, short, specific fragments of a known gene are amplifiedsubsequent to a bisulfite treatment and either completely sequenced(Olek A, Walter J. The pre-implantation ontogeny of the HI 9 methylationimprint. Nat Genet. 1997 November; 17(3):275-6) or individual cytosinepositions are detected by a primer extension reaction (Gonzalgo M L,Jones P A. Rapid quantitation of methylation differences at specificsites using methylation-sensitive single nucleotide primer extension(Ms-SNuPE). Nucleic Acids Res. 1997 Jun. 15; 25(12):2529-31, WO95/00669) or by enzymatic digestion (Xiong Z, Laird P W. COBRA: asensitive and quantitative DNA methylation assay. Nucleic Acids Res.1997 Jun. 15; 25(12):2532-4). In addition, detection by hybridisationhas also been described (Olek et al., WO 99/28498).

Further publications dealing with the use of the bisulfite technique formethylation detection in individual genes are: Grigg G, Clark S.Sequencing 5-methylcytosine residues in genomic DNA. Bioessays. 1994June; 16(6):431-6, 431; Zeschnigk M, Schmitz B, Dittrich B, Buffing K,Horsthemke B, Doerfler W. Imprinted segments in the human genome:different DNA methylation patterns in the Prader-Willi/Angelman syndromeregion as determined by the genomic sequencing method. Hum Mol Genet.1997 March; 6(3):387-95; Feil R, Charlton J, Bird A P, Walter J, Reik W.Methylation analysis on individual chromosomes: improved protocol forbisulphite genomic sequencing. Nucleic Acids Res. 1994 Feb. 25;22(4):695-6; Martin V, Ribieras S, Song-Wang X, Rio M C, Dante R.Genomic sequencing indicates a correlation between DNA hypomethylationin the 5′ region of the pS2 gene and its expression in human breastcancer cell lines. Gene. 1995 May 19; 157(1-2):261-4; WO 97/46705 and WO95/15373.

An overview of the Prior Art in oligomer array manufacturing can begathered from a special edition of Nature Genetics (Nature GeneticsSupplement, Volume 21, January 1999), published in January 1999, andfrom the literature cited therein.

Fluorescently labelled probes are often used for the scanning ofimmobilised DNA arrays. The simple attachment of Cy3 and Cy5 dyes to the5′-OH of the specific probe are particularly suitable for fluorescencelabels. The detection of the fluorescence of the hybridised probes maybe carried out, for example via a confocal microscope. Cy3 and Cy5 dyes,besides many others, are commercially available.

Matrix Assisted Laser Desorption Ionization Mass Spectrometry(MALDI-TOF) is a very efficient development for the analysis ofbiomolecules (Karas M, Hillenkamp F. Laser desorption ionisation ofproteins with molecular masses exceeding 10,000 daltons. Anal Chem. 1988Oct. 15; 60(20):2299-301). An analyte is embedded in a light-absoRBingmatrix. The matrix is evaporated by a short laser pulse thustransporting the analyte molecule into the vapour phase in anunfragmented manner. The analyte is ionised by collisions with matrixmolecules. An applied voltage accelerates the ions into a field-freeflight tube. Due to their different masses, the ions are accelerated atdifferent rates. Smaller ions reach the detector sooner than biggerones.

MALDI-TOF spectrometry is excellently suited to the analysis of peptidesand proteins. The analysis of nucleic acids is somewhat more difficult(Gut I G, Beck S. DNA and Matrix Assisted Laser Desorption IonisationMass Spectrometry. Current Innovations and Future Trends. 1995, 1;147-57). The sensitivity to nucleic acids is approximately 100 timesworse than to peptides and decreases disproportionally with increasingfragment size. For nucleic acids having a multiply negatively chargedbackbone, the ionisation process via the matrix is considerably lessefficient. In MALDI-TOF spectrometry, the selection of the matrix playsan eminently important role. For the desorption of peptides, severalvery efficient matrixes have been found which produce a very finecrystallisation. There are now several responsive matrixes for DNA,however, the difference in sensitivity has not been reduced. Thedifference in sensitivity can be reduced by chemically modifying the DNAin such a manner that it becomes more similar to a peptide.Phosphorothioate nucleic acids in which the usual phosphates of thebackbone are substituted with thiophosphates can be converted into acharge-neutral DNA using simple alkylation chemistry (Gut I G, Beck S. Aprocedure for selective DNA alkylation and detection by massspectrometry. Nucleic Acids Res. 1995 Apr. 25; 23(8):1367-73). Thecoupling of a charge tag to this modified DNA results in an increase insensitivity to the same level as that found for peptides. A furtheradvantage of charge tagging is the increased stability of the analysisagainst impurities which make the detection of unmodified substratesconsiderably more difficult.

Genomic DNA is obtained from DNA of cell, tissue or other test samplesusing standard methods. This standard methodology is found in referencessuch as Sambrook, Fritsch and Maniatis eds., Molecular Cloning: ALaboratory Manual, 1989.

DESCRIPTION

The invention provide a method for the analysis of biological samplesfor features associated with the development of colon cell proliferativedisorders, characterised in that the nucleic acid of at least one memberof the group comprising MDR1, APOC2, CACNA1G, EGR4, AR, RB1, GPIb beta,MYOD1, WT1, HLA-F, ELK1, APC, BCL2, CALCA, CDH1, CDKN1A, CDKN1B (p27Kip1), CDKN2a, CDKN2B, CD44, CSPG2, DAPK1, EGFR, EYA4, GSTP1, GTBP/MSH6,HIC-1, HRAS, IGF2, LKB1, MGMT, MLH1, MNCA9, MSH3, MYC, N33, PAX6, PGR,PTEN, RARB, SFN, S100A2, TGFBR2, TIMP3, TP53, TP73, VHL, CDKN1C, CAV1,CDH13, DRG1, PTGS2, THBS1, TPEF (=TMEFF2; =HPP1), DNMT1, CEA, MB, PCNA,CDC2, ESR1, CASP8, RASSF1, MSH4, MSH5 is/are contacted with a reagent orseries of reagents capable of distinguishing between methylated and nonmethylated CpG dinucleotides within the genomic sequence of interest.

The present invention makes available a method for ascertaining geneticand/or epigenetic parameters of genomic DNA. The method is for use inthe improved diagnosis, treatment and monitoring of colon cellproliferative disorders, more specifically by enabling the improvedidentification of and differentiation between subclasses of saiddisorder and the genetic pre-disposition to said disorders. Theinvention presents improvements over the state of the art in that itenables a highly specific classification of colon carcinomas, therebyallowing for improved and informed treatment of patients.

In a particularly preferred embodiment the present invention makesavailable methods and nucleic acids that allow the differentiationbetween colon carcinoma, colon adenoma and normal colon tissue.

Furthermore, the method enables the analysis of cytosine methylationsand single nucleotide polymorphisms.

The genes that form the basis of the present invention can be used toform a “gene panel”, i.e. a collection comprising the particular geneticsequences of the present invention and/or their respective informativemethylation sites. The formation of gene panels allow for a quick andspecific analysis of the disorders they are related with. The genepanels described in this invention can be used with surprisingly highefficiency for the diagnosis, treatment and monitoring of and theanalysis of colon cell proliferative disorders as described herein. Theuse of multiple CpG sites from a diverse array of genes, allows for arelatively high degree of sensitivity and specificity in comparison tosingle gene diagnostic and detection tools. Furthermore, the panel asdescribed herein may be adapted for use in the analysis of many aspectsof colon cell proliferative disorders.

In a preferred embodiment, the method comprises the following steps:

In the first step of the method the genomic DNA sample must be isolatedfrom tissue or cellular sources. Such sources may include colon tissuesamples, cell lines, histological slides, body fluids, or tissueembedded in paraffin. Extraction may be by means that are standard toone skilled in the art, these include the use of detergent lysates,sonification and vortexing with glass beads. Once the nucleic acids havebeen extracted the genomic double stranded DNA is used in the analysis.

In a preferred embodiment the DNA may be cleaved prior to the next stepof the method, this may be by any means standard in the state of theart, in particular, but not limited to, with restriction endonucleases.

In the second step of the method, the genomic DNA sample is treated insuch a manner that cytosine bases which are unmethylated at the5′-position are converted to uracil, thymine, or another base which isdissimilar to cytosine in terms of hybridisation behaviour. This will beunderstood as ‘pretreatment’ hereinafter.

The above described treatment of genomic DNA is preferably carried outwith bisulfite (sulfite, disulfite) and subsequent alkaline hydrolysiswhich results in a conversion of non-methylated cytosine nucleobases touracil or to another base which is dissimilar to cytosine in terms ofbase pairing behaviour. If bisulfite solution is used for the reaction,then an addition takes place at the non-methylated cytosine bases.Moreover, a denaturating reagent or solvent as well as a radicalinterceptor must be present. A subsequent alkaline hydrolysis then givesrise to the conversion of non-methylated cytosine nucleobases to uracil.The chemically converted DNA is then used for the detection ofmethylated cytosines.

Fragments of the pretreated DNA are amplified, using sets of primeroligonucleotides according to SEQ ID NO: 389 to SEQ ID NO: 518, and a,preferably heat-stable, polymerase. Because of statistical and practicalconsiderations, preferably more than ten different fragments having alength of 100-2000 base pairs are amplified. The amplification ofseveral DNA segments can be carried out simultaneously in one and thesame reaction vessel. Usually, the amplification is carried out by meansof a polymerase chain reaction (PCR).

The method may also be enabled by the use of alternative primers, thedesign of such primers is obvious to one skilled in the art. Theseshould include at least two oligonucleotides whose sequences are eachreverse complementary or identical to an at least 18 base-pair longsegment of the base sequences specified in the appendix (SEQ ID NO: 133to SEQ ID NO: 388). Said primer oligonucleotides are preferablycharacterised in that they do not contain any CpG dinucleotides. In aparticularly preferred embodiment of the method, the sequence of saidprimer oligonucleotides are designed so as to selectively anneal to andamplify, only the colon tissue specific DNA of interest, therebyminimising the amplification of background or non relevant DNA. In thecontext of the present invention, background DNA is taken to meangenomic DNA which does not have a relevant tissue specific methylationpattern, in this case, the relevant tissue being colon, both healthy anddiseased.

According to the present invention, it is preferred that at least oneprimer oligonucleotide is bound to a solid phase during amplification.The different oligonucleotide and/or PNA-oligomer sequences can bearranged on a plane solid phase in the form of a rectangular orhexagonal lattice, the solid phase surface preferably being composed ofsilicon, glass, polystyrene, aluminium, steel, iron, copper, nickel,silver, or gold, it being possible for other materials such asnitrocellulose or plastics to be used as well.

The fragments obtained by means of the amplification can carry adirectly or indirectly detectable label. Preferred are labels in theform of fluorescence labels, radionuclides, or detachable moleculefragments having a typical mass which can be detected in a massspectrometer, it being preferred that the fragments that are producedhave a single positive or negative net charge for better detectabilityin the mass spectrometer. The detection may be carried out andvisualised by means of matrix assisted laser desorption/ionisation massspectrometry (MALDI) or using electron spray mass spectrometry (ESI).

The amplificates obtained in the second step of the method aresubsequently hybridised to an array or a set of oligonucleotides and/orPNA probes. In this context, the hybridisation preferably takes place inthe manner described as follows. The set of probes used during thehybridisation is preferably composed of at least 10 oligonucleotides orPNA-oligomers. However, it is understood and as well claimed, that theprocess can be conducted using only one Oligonucleotide or PNA probe. Inthe process, the amplificates hybridise to oligonucleotides previouslybonded to a solid phase. In a particularly preferred embodiment, theoligonucleo-tides are taken from the group comprising SEQ ID NO: 519 toSEQ ID NO: 1030. In a further preferred embodiment the oligonucleotidesare taken from the group comprising SEQ ID NO: 895 to SEQ ID NO: 1030.The non-hybridised fragments are subsequently removed. Saidoligonucleotides contain at least one base sequence having a length of10 nucleotides which is reverse complementary or identical to a segmentof the base sequences specified in the appendix, the segment containingat least one CpG or TpG dinucleotide. In a further preferred embodimentthe cytosine of the CpG dinucleotide, or in the case of TpG, thethiamine, is the 5^(th) to 9^(th) nucleotide from the 5′-end of the10-mer. One oligonucleotide exists for each CpG or TpG dinucleotide.

In the fifth step of the method, the non-hybridised amplificates areremoved.

In the final step of the method, the hybridised amplificates aredetected. In this context, it is preferred that labels attached to theamplificates are identifiable at each position of the solid phase atwhich an oligonucleotide sequence is located.

According to the present invention, it is preferred that the labels ofthe amplificates are fluorescence labels, radionuclides, or detachablemolecule fragments having a typical mass which can be detected in a massspectrometer. The mass spectrometer is preferred for the detection ofthe amplificates, fragments of the amplificates or of probes which arecomplementary to the amplificates, it being possible for the detectionto be carried out and visualised by means of matrix assisted laserdesorption/ionisation mass spectrometry (MALDI) or using electron spraymass spectrometry (ESI). The produced fragments may have a singlepositive or negative net charge for better detectability in the massspectrometer.

The aforementioned method is preferably used for ascertaining geneticand/or epigenetic parameters of genomic DNA.

In order to enable this method, the invention further provides themodified DNA of genes MDR1, APOC2, CACNA1G, EGR4, AR, RB1, GPIb beta,MYOD1, WT1, HLA-F, ELK1, APC, BCL2, CALCA, CDH1, CDKN1A, CDKN1B (p27Kip1), CDKN2a, CDKN2B, CD44, CSPG2, DAPK1, EGFR, EYA4, GSTP1, GTBP/MSH6,HIC-1, HRAS, IGF2, LKB1, MGMT, MLH1, MNCA9, MSH3, MYC, N33, PAX6, PGR,PTEN, RARB, SFN, S100A2, TGFBR2, TIMP3, TP53, TP73, VHL, CDKN1C, CAV1,CDH13, DRG1, PTGS2, THBS1, TPEF (=TMEFF2; =HPP1), DNMT1, CEA, MB, PCNA,CDC2, ESR1, CASP8, RASSF1, MSH4, MSH5 as well as oligonucleotides and/orPNA-oligomers for detecting cytosine methylations within said genes. Thepresent invention is based on the discovery that genetic and epigeneticparameters and, in particular, the cytosine methylation patterns ofgenomic DNA are particularly suitable for improved diagnosis, treatmentand monitoring of colon cell proliferative disorders. Furthermore, theinvention enables the differentiation between different subclasses ofcolon cell proliferative disorders or detection of a predisposition tocolon cell proliferative disorders.

The nucleic acids according to the present invention can be used for theanalysis of genetic and/or epigenetic parameters of genomic DNA.

This objective is achieved according to the present invention using anucleic acid containing a sequence of at least 18 bases in length of thepretreated genomic DNA according to one of SEQ ID NO: 133 to SEQ ID NO:388 and sequences complementary thereto.

The modified nucleic acid could heretofore not be connected with theascertainment of disease relevant genetic and epigenetic parameters.

The object of the present invention is further achieved by anoligonucleotide or oligomer for the analysis of pretreated DNA, fordetecting the genomic cytosine methylation state, said oligonucleotidecontaining at least one base sequence having a length of at least 10nucleotides which hybridises to a pretreated genomic DNA according toSEQ ID NO: 133 through to SEQ ID NO: 388. The oligomer probes accordingto the present invention constitute important and effective tools which,for the first time, make it possible to ascertain specific genetic andepigenetic parameters during the analysis of biological samples forfeatures associated with the development of colon cell proliferativedisorders. Said oligonucleotides allow the improved diagnosis, treatmentand monitoring of colon cell proliferative disorders and detection ofthe predisposition to said disorders. Furthermore, they allow thedifferentiation of different subclasses of colon cell proliferativedisorders. The base sequence of the oligomers preferably contains atleast one CpG or TpG dinucleotide. The probes may also exist in the formof a PNA (peptide nucleic acid) which has particularly preferred pairingproperties. Particularly preferred are oligonucleotides according to thepresent invention in which the cytosine of the CpG dinucleotide is the5^(th)-9^(th) nucleotide from the 5′-end of the 13-mer; in the case ofPNA-oligomers, it is preferred for the cytosine of the CpG dinucleotideto be the 4th-6th nucleotide from the 5′-end of the 9-mer.

The oligomers according to the present invention are normally used in socalled “sets” which contain at least one oligomer for each of the CpGdinucleotides within SEQ ID NO: 133 through SEQ ID NO: 388. Preferred isa set which contains at least one oligomer for each of the CpGdinucleotides, from SEQ ID NO: 519 to SEQ ID NO: 1030. Further preferredis a set comprising SEQ ID NO: 895 to SEQ ID NO: 1030.

In the case of the sets of oligonucleotides according to the presentinvention, it is preferred that at least one oligonucleotide is bound toa solid phase. It is further preferred that all the oligonucleotides ofone set are bound to a solid phase.

The present invention moreover relates to a set of preferably at least10 n (oligonucleotides and/or PNA-oligomers) used for detecting thecytosine methylation state of genomic DNA using treated versions of saidgenomic DNA (according to SEQ ID NO: 133 to SEQ ID NO: 388 and sequencescomplementary thereto). However, it is understood and as well claimed,that the process can be conducted using only one Oligonucleotide or PNAoligomer. These probes enable improved diagnosis, treatment andmonitoring of colon cell proliferative disorders. In particular theyenable the differentiation between different sub classes of colon cellproliferative disorders and the detection of a predisposition to saiddisorders. In a particularly preferred embodiment the set comprises SEQID NO: 519 to SEQ ID NO: 1030.

The set of oligomers may also be used for detecting single nucleotidepolymorphisms (SNPs) using pretreated genomic DNA according to one ofSEQ ID NO: 133 to SEQ ID NO: 388.

According to the present invention, it is preferred that an arrangementof different oligonucleotides and/or PNA-oligomers (a so-called “array”)made available by the present invention is present in a manner that itis likewise bound to a solid phase. This array of differentoligonucleotide- and/or PNA-oligomer sequences can be characterised inthat it is arranged on the solid phase in the form of a rectangular orhexagonal lattice. The solid phase surface is preferably composed ofsilicon, glass, polystyrene, aluminium, steel, iron, copper, nickel,silver, or gold. However, nitrocellulose as well as plastics such asnylon which can exist in the form of pellets or also as resin matricesare suitable alternatives.

Therefore, a further subject matter of the present invention is a methodfor manufacturing an array fixed to a carrier material for the improveddiagnosis, treatment and monitoring of colon cell proliferativedisorders, the differentiation between different subclasses of coloncell proliferative disorders and/or detection of the predisposition tocolon cell proliferative disorders. In said method at least one oligomeraccording to the present invention is coupled to a solid phase. Methodsfor manufacturing such arrays are known, for example, from U.S. Pat. No.5,744,305 by means of solid-phase chemistry and photolabile protectinggroups.

A further subject matter of the present invention relates to a DNA chipfor the improved diagnosis, treatment and monitoring of colon cellproliferative disorders. Furthermore the DNA chip enables detection ofthe predisposition to colon cell proliferative disorders and thedifferentiation between different subclasses of colon cell proliferativedisorders. The DNA chip contains at least one nucleic acid according tothe present invention. DNA chips are known, for example, in U.S. Pat.No. 5,837,832.

Moreover, a subject matter of the present invention is a kit which maybe composed, for example, of a bisulfite-containing reagent, a set ofprimer oligonucleotides containing at least two oligonucleotides whosesequences in each case correspond or are complementary to a 18 base longsegment of the base sequences specified in the appendix (SEQ ID NO: 133to SEQ ID NO: 388), oligonucleotides and/or PNA-oligomers as well asinstructions for carrying out and evaluating the described method.However, a kit along the lines of the present invention can also containonly part of the aforementioned components.

The oligomers according to the present invention or arrays thereof aswell as a kit according to the present invention are intended to be usedfor the improved diagnosis, treatment and monitoring of colon cellproliferative disorders. Furthermore the use of said inventions extendsto the differentiation between different subclasses of colon cellproliferative disorders and detection of the predisposition to coloncell proliferative disorders. According to the present invention, themethod is preferably used for the analysis of important genetic and/orepigenetic parameters within genomic DNA, in particular for use inimproved diagnosis, treatment and monitoring of colon cell proliferativedisorders, detection of the predisposition to said disorders and thedifferentiation between subclasses of said disorders.

The methods according to the present invention are vised, for example,for improved diagnosis, treatment and monitoring of colon cellproliferative disorders progression, detection of the predisposition tosaid disorders and the differentiation between subclasses of saiddisorders. A further embodiment of the invention is a method for theanalysis of the methylation status of genomic DNA without the need forpretreatment. In the first step of the method the genomic DNA samplemust be isolated from tissue or cellular sources. Such sources mayinclude cell lines, histological slides, body fluids, or tissue embeddedin paraffin. Extraction may be by means that are standard to one skilledin the art, these include the use of detergent lysates, sonification andvortexing with glass beads. Once the nucleic acids have been extractedthe genomic double stranded DNA is used in the analysis.

In a preferred embodiment the DNA may be cleaved prior to the treatment,this may be any means standard in the state of the art, in particularwith restriction endonucleases. In the second step, the DNA is thendigested with one or more methylation sensitive restriction enzymes. Thedigestion is carried out such that hydrolysis of the DNA at therestriction site is informative of the methylation status of a specificCpG dinucleotide.

In the third step the restriction fragments are amplified. In apreferred embodiment this is carried out using a polymerase chainreaction.

In the final step the amplificates are detected. The detection may be byany means standard in the art, for example, but not limited to, gelelectrophoresis analysis, hybridisation analysis, incorporation ofdetectable tags within the PCR products, DNA array analysis, MALDI orESI analysis.

The present invention moreover relates to the diagnosis and/or prognosisof events which are disadvantageous or relevant to patients orindividuals in which important genetic and/or epigenetic parameterswithin genomic DNA, said parameters obtained by means of the presentinvention may be compared to another set of genetic and/or epigeneticparameters, the differences serving as the basis for the diagnosisand/or prognosis of events which are disadvantageous or relevant topatients or individuals.

In the context of the present invention the term “hybridisation” is tobe understood as a bond of an oligonucleotide to a completelycomplementary sequence along the lines of the Watson-Crick base pairingsin the sample DNA, forming a duplex structure.

In the context of the present invention, “genetic parameters” aremutations and polymorphisms of genomic DNA and sequences furtherrequired for their regulation. To be designated as mutations are, inparticular, insertions, deletions, point mutations, inversions andpolymorphisms and, particularly preferred, SNPs (single nucleotidepolymorphisms).

In the context of the present invention “methylation state analysis” istaken to mean the analysis of cytosines within a nucleic acid in orderto ascertain whether they are methylated or not. In the context of thepresent invention, “epigenetic parameters” are, in particular, cytosinemethylations and further modifications of DNA bases of genomic DNA andsequences further required for their regulation. Further epigeneticparameters include, for example, the acetylation of histones which,cannot be directly analysed using the described method but which, inturn, correlates with the DNA methylation.

In the following, the present invention will be explained in greaterdetail on the basis of the sequences and examples without being limitedthereto.

SEQ ID NO: 1 to SEQ ID NO: 64 represent 5′ and/or regulatory regions ofthe genomic DNA of genes MDR1, APOC2, CACNA1G, EGR4, AR, RB1, GPIb beta,MYOD1, WT1, HLA-F, ELK1, APC, BCL2, CALCA, CDH1, CDKN1A, CDKN1B (p27Kip1), CDKN2a, CDKN2B, CD44, CSPG2, DAPK1, EGFR, EYA4, GSTP1, GTBP/MSH6,HIC-1, HRAS, IGF2, LKB1, MGMT, MLH1, MNCA9, MSH3, MYC, N33, PAX6, PGR,PTEN, RARB, SFN, S100A2, TGFBR2, TIMP3, TP53, TP73, VHL, CDKN1C, CAV1,CDH13, DRG1, PTGS2, THBS1, TPEF (=TMEFF2; =HPP1), DNMT1, CEA, MB, PCNA,CDC2, ESR1, CASP8, RASSF1, MSH4, MSH5. These sequences are derived fromthe ensembl database (date 01.10.2001) (http://www.ensembl.org) and willbe taken to include all minor variations of the sequence material whichare currently unforeseen, for example, but not limited to, minordeletions and SNPs.

SEQ ID 133 to 388 exhibit the pretreated sequences of DNA derived fromgenes MDR1, APOC2, CACNA1G, EGR4, AR, RB1, GPIb beta, MYOD1, WT1, HLA-F,ELK1, APC, BCL2, CALCA, CDH1, CDKN1A, CDKN1B (p27 Kip1), CDKN2a, CDKN2B,CD44, CSPG2, DAPK1, EGFR, EYA4, GSTP1, GTBP/MSH6, HIC-1, HRAS, IGF2,LKB1, MGMT, MLH1, MNCA9, MSH3, MYC, N33, PAX6, PGR, PTEN, RARE, SFN,S100A2, TGFBR2, TIMP3, TP53, TP73, VHL, CDKN1C, CAV1, CDH13, DRG1,PTGS2, THBS1, TPEF (=TMEFF2; =HPP1), DNMT1, CEA, MB, PCNA, CDC2, ESR1,CASP8, RASSFI, MSH4, MSH5. These sequences will be taken to include allminor variations of the sequence material which are currentlyunforeseen, for example, but not limited to, minor deletions and SNPs.

SEQ ID NO: 389 to SEQ ID NO: 518 exhibit the sequences of primeroligonucleotides for the amplification of pretreated DNA according toSequence ID NO: 133 to SEQ ID NO: 388.

SEQ ID NO: 65 to SEQ ID NO: 132 exhibit the sequences of oligomers whichare useful for the analysis of CpG positions within genomic DNAaccording to SEQ ID NO: 1 to SEQ ID NO: 64.

SEQ ID NO: 519 to SEQ ID NO: 1030 exhibit the sequences of oligomerswhich are useful for the analysis of the methylation status of CpGpositions within genomic DNA according to SEQ ID NO: 1 to SEQ ID NO: 64after treatment of said genomic DNA with bisulfate.

SEQ ID NO: 895 to SEQ ID NO: 1030 exhibit the sequences of oligomerswhich are particularly useful for the analysis of CpG positions withingenomic DNA according to SEQ ID NO: 1 to SEQ ID NO: 64, after treatmentof said with bisulfate and are subject to a preferred embodiment of thisinvention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Differentiation between healthy colon tissue and adenoma orcarcinoma colon tissue according to Example 2. The labels on the leftside of the plot are gene and CpG identifiers, these can be crossreferenced using Table 3 and Table 7. The labels on the right side ofthe figure give the significance (p-value, T-test) of the differencebetween the means of the two groups. Each row corresponds to a singleCpG and each column to the methylation levels of one sample. CpGs areordered according to their contribution to the differentiation betweenthe two tissue types (A=healthy, B=non healthy) with increasingcontribution from top to bottom. Black indicates total methylation at agiven CpG position, white represents no methylation at the particularposition, with degrees of methylation represented in grey, from light(low proportion of methylation) to dark (high proportion ofmethylation).

FIG. 2: Differentiation between healthy colon tissue and carcinoma colontissue according to Example 2. The labels on the left side of the plotare gene and CpG identifiers, these can be cross referenced using Table4 and Table 7. The labels on the right side of the figure give thesignificance (p-value, T-test) of the difference between the means ofthe two groups. Each row corresponds to a single CpG and each column tothe methylation levels of one sample. CpGs are ordered according totheir contribution to the differentiation between the two tissue types(A=healthy, B=carcinoma) with increasing contribution from top tobottom. Black indicates total methylation at a given CpG position, whiterepresents no methylation at the particular position, with degrees ofmethylation represented in grey, from light (low proportion ofmethylation) to dark (high proportion of methylation).

FIG. 3: Differentiation between healthy colon tissue and adenoma colontissue according to Example 2. The labels on the left side of the plotare gene and CpG identifiers, these can be cross referenced in Table 5and Table 7. The labels on the right side give the significance(p-value, T-test) of the difference between the means of the two groups.Each row corresponds to a single CpG and each column to the methylationlevels of one sample. CpGs are ordered according to their contributionto the distinction to the differential diagnosis between the two tissuetypes (A=healthy, B=adenoma) with increasing contribution from top tobottom.

Black indicates total methylation at a given CpG position, whiterepresents no methylation at the particular position, with degrees ofmethylation represented in grey, from light (low proportion ofmethylation) to dark (high proportion of methylation). Due to formattingof the page only 40 CpGs are shown in this figure.

FIG. 4: Differentiation between carcinoma colon tissue and adenoma colontissue according to Example 2. The labels on the left side of the plotare gene and CpG identifiers, these can be cross referenced in Table 6and Table 7. The labels on the right side give the significance(p-value, T-test) of the difference between the means of the two groups.Each row corresponds to a single CpG and each column to the methylationlevels of one sample. CpGs are ordered according to their contributionto the distinction to the differential diagnosis between the two tissuetypes (A=carcinoma, B=adenoma) with increasing contribution from top tobottom. Black indicates total methylation at a given CpG position, whiterepresents no methylation at the particular position, with degrees ofmethylation represented in grey, from light (low proportion ofmethylation) to dark (high proportion of methylation).

EXAMPLES 1 AND 2 Digital Phenotype

In the following examples, multiplex PCR was carried out upon tissuesamples originating from colon adenomas or colon carcinoma. MultiplexPCR was also carried out upon healthy colon tissue. Each sample wastreated in the manner described below in Example 1 in order to deducethe methylation status of CpG positions, the CpG methylation informationfor each sample was collated and then used in an analysis, as detailedin Example 2. An alternative method for the analysis of CpG methylationstatus is described in Example 3.

EXAMPLE 1

In the first step the genomic DNA was isolated from the cell samplesusing the Wizzard kit from (Promega).

The isolated genomic DNA from the samples are treated using a bisulfatesolution (hydrogen sulfite, disulfite). The treatment is such that allnon methylated cytosines within the sample are converted to thiamidine,conversely 5-methylated cytosines within the sample remain unmodified.

The treated nucleic acids were then amplified using multiplex PCRs,amplifying 8 fragments per reaction with Cy5 fluorescently labelledprimers. PCR primers used are described in Table 1. PCR conditions wereas follows.

Reaction Solution:

10 ng bisulfite treated DNA

3.5 mM MgCl2

400 μM dNTPs2 pmol each primer

1 U Hot Star Taq (Qiagen)

Forty cycles were carried out as follows. Denaturation at 95° C. for 15min, followed by annealing at 55° C. for 45 sec., primer elongation at65° C. for 2 min. A final elongation at 65° C. was carried out for 10min.

All PCR products from each individual sample were then hybridised toglass slides carrying a pair of immobilised oligonucleotides for eachCpG position under analysis. Each of these detection oligonucleotideswas designed to hybridise to the bisulphite converted sequence aroundone CpG site which was either originally unmethylated (TG) or methylated(CG). See Table 2 for further details of all hybridisationoligonucleotides used (both informative and non-informative)Hybridisation conditions were selected to allow the detection of thesingle nucleotide differences between the TG and CG variants.

5 μl volume of each multiplex PCR product was diluted in 10×Ssarc buffer(10×Ssarc:230 ml 20×SSC, 180 ml sodium lauroyl sarcosinate solution 20%,dilute to 1000 ml with dH20). The reaction mixture was then hybridisedto the detection oligonucleotides as follows. Denaturation at 95° C.,cooling down to 10° C., hybridisation at 42° C. overnight followed bywashing with 10×Ssarc and dH20 at 42° C.

Fluorescent signals from each hybridised oligonucleotide were detectedusing genepix scanner and software. Ratios for the two signals (from theCG oligonucleotide and the TG oligonucleotide used to analyse each CpGposition) were calculated based on comparison of intensity of thefluorescent signals.

EXAMPLE 2

The data obtained according to Example 1 is then sorted into a rankedmatrix (as shown in FIGS. 1 to 4) according to CpG methylationdifferences between the two classes of tissues, using an algorithm. Themost significant CpG positions are at the bottom of the matrix withsignificance decreasing towards the top. Black indicates totalmethylation at a given CpG position, white represents no methylation atthe particular position, with degrees of methylation represented ingrey, from light (low proportion of methylation) to dark (highproportion of methylation). Each row represents one specific CpGposition within a gene and each column shows the methylation profile forthe different CpGs for one sample. On the left side a CpG and geneidentifier is shown this may be cross referenced with the accompanyingtables (Table 1 and 7) in order to ascertain the gene in question andthe detection oligomer vised. On the right side p values for theindividual CpG positions are shown. The p values are the probabilitiesthat the observed distribution occurred by chance in the data set.

For selected distinctions, we trained a learning algorithm (supportvector machine, SVM). The SVM (as discussed by F. Model, P. Adoijan, A.Olek, C. Piepenbrock, Feature selection for DNA methylation based cancerclassification. Bioinformatics. 2001 June; 17 Suppl 1:S157-64)constructs an optimal discriminant between two classes of given trainingsamples. In this case each sample is described by the methylationpatterns (CG/TG ratios) at the investigated CpG sites. The SVM wastrained on a subset of samples of each class, which were presented withthe diagnosis attached. Independent test samples, which were not shownto the SVM before were then presented to evaluate, if the diagnosis canbe predicted correctly based on the predictor created in the traininground. This procedure was repeated several times using differentpartitions of the samples, a method called cross-validation. Please notethat all rounds are performed without using any knowledge obtained inthe previous runs. The number of correct classifications was averagedover all runs, which gives a good estimate of our test accuracy (percentof correct classified samples over all rounds).

Healthy Colon Tissue Compared to Non Healthy Colon Tissue (Colon Adenomaand Colon Carcinoma) (FIG. 1)

FIG. 1 shows the differentiation of healthy tissue from non healthytissue wherein the non healthy specimens are obtained from either colonadenoma or colon carcinoma tissue. The evaluation is carried out usinginformative CpG positions from 27 genes. Informative CpG positions arefurther described in Table 3.

Healthy Colon Tissue Compared to Colon Carcinoma Tissue (FIG. 2)

FIG. 2 shows the differentiation of healthy tissue from carcinoma tissueusing informative CpG positions from 15 genes. Informative CpG positionsare further described in Table 4.

Healthy Colon Tissue Compared to Colon Adenoma Tissue (FIG. 3)

FIG. 3 shows the differentiation of healthy tissue from adenoma tissueusing informative CpG positions from 40 genes. Informative CpG positionsare further described in Table 5.

Colon Carcinoma Tissue Compared to Colon Adenoma Tissue (FIG. 4)

FIG. 4 shows the differentiation of carcinoma tissue from adenoma tissueusing informative CpG positions from 2 genes. Informative CpG positionsare further described in Table 6.

EXAMPLE 3 Identification of the Methylation Status of a CPG Site withinthe Gene CD44

A fragment of the bisulfate treated DNA of the gene CD44 (Seq ID NO: 20)was PCR amplified using primers GAAAGGAGAGGTTAAAGGTTG (Seq ID NO 429)and AACTCACTTAACTCCAATCCC (Seq ID NO 430). The resultant fragment (696bp in length) contained an informative CpG at position 235. Theamplificate DNA was digested with the restriction endonuclease Apa I,recognition site GGGCC. Hydrolysis by said endonuclease is blocked bymethylation of the CpG at position 235 of the amplificate. The digestwas used as a control.

Genomic DNA was isolated from sample using the DNA wizzard DNA isolationkit (Pro-mega). Each sample was digested using Apa I according tomanufacturer's recommendations (New England Biolabs).

10 ng of each genomic digest was then amplified using PCR primersGAAAGGAGAGGTTAAAGGTTG and AACTCACTTAACTCCAATCCC. The PCR reactions wereperformed using a thermocycler (Eppendorf GmbH) using 10 ng of DNA, 6pmol of each primer, 200 μM of each dNTP, 1.5 mM MgCl2 and 1 U ofHotstartTaq (Qiagen AG). The other conditions were as recommended by theTaq polymerase manufacturer. Using the above mentioned primers, genefragments were amplified by PCR performing a first denaturation step for14 min at 96° C., followed by 30-45 cycles (step 2: 60 sec at 96° C.,step 3: 45 sec at 52° C., step 4: 75 sec at 72° C.) and a subsequentfinal elongation of 10 min at 72° C. The presence of PCR products wasanalysed by agarose gel electrophoresis.

PCR products were detectable with Apa I hydrolysed DNA isolated whereinthe CpG position in question was up-methylated, when step 2 to step 4 ofthe cycle program were repeated 34, 37, 39, 42 and 45 fold. In contrastPCR products were only detectable with Apa I hydrolysed DNA isolatedfrom down-methylated DNA (and control DNA) when step 2 to step 4 of thecycle program were repeated 42 and 45 fold. These results wereincorporated into a CpG methylation matrix analysis as described inExample 2.

Tables

TABLE 1 PCR primers and products Amplificate No: Gene: Primer: Length: 1MDR1 TAAGTATGTTGAAGAAAGATTATTGTAG 633 (SEQ ID NO: 1) (SEQ ID NO: 389)TAAAAACTATCCCATAATAACTCCCAAC (SEQ ID NO: 390) 2 APOC2ATGAGTAGAAGAGGTGATAT 533 (SEQ ID NO: 2) (SEQ ID NO: 391)CCCTAAATCCCTTTCTTACC (SEQ ID NO: 392) 3 CACNA1G GGGATTTAAGAGAAATTGAGGTA707 (SEQ ID NO: 3) (SEQ ID NO: 393) AAACCCCAAACATCCTTTAT(SEQ ID NO: 394) 4 EGR4 AGGGGGATTGAGTGTTAAGT 293 (SEQ ID NO: 4)(SEQ ID NO: 395) CCCAAACATAAACACAAAAT (SEQ ID NO: 396) 5 ARGTAGTAGTAGTAGTAAGAGA 460 (SEQ ID NO: 5) (SEQ ID NO: 397)ACCCCCTAAATAATTATCCT (SEQ ID NO: 398) 6 RB1 TTTAAGTTTGTTTTTGTTTTGGT 718(SEQ ID NO: 6) (SEQ ID NO: 399) TCCTACTCTAAATCCTCCTCAA (SEQ ID NO: 400)7 GPIb beta GGTGATAGGAGAATAATGTTGG 379 (SEQ ID NO: 7) (SEQ ID NO: 401)TCTCCCAACTACAACCAAAC (SEQ ID NO: 402) 8 MYOD1 ATTAGGGGTATAGAGGAGTATTGA883 (SEQ ID NO: 8) (SEQ ID NO: 403) CTTACAAACCCACAATAAACAA(SEQ ID NO: 404) 9 WT1 AAAGGGAAATTAAGTGTTGT 747 (SEQ ID NO: 9)(SEQ ID NO: 405) TAACTACCCTCAACTTCCC (SEQ ID NO: 406) 10 HLA-FTTGTTGTTTTTAGGGGTTTTGG 946 (SEQ ID NO: 10) (SEQ ID NO: 407)TCCTTCCCATTCTCCAAATATC (SEQ ID NO: 408) 11 ELK1 AAGTGTTTTAGTTTTTAATGGGTA966 (SEQ ID NO: 11) (SEQ ID NO: 409) CAAACCCAAAACTCACCTAT(SEQ ID NO: 410) 12 APC TCAACTACCATCAACTTCCTTA 491 (SEQ ID NO: 12)(SEQ ID NO: 411) AATTTATTTTTAGTGTTGTAGTGGG (SEQ ID NO: 412) 13 BCL2GTATTTTATGTTAAGGGGGAAA 640 (SEQ ID NO: 13) (SEQ ID NO: 413)AAAAACCACAATCCTCCC (SEQ ID NO: 414) 14 CALCA GTTTTGGAAGTATGAGGGTG 614(SEQ ID NO: 14) (SEQ ID NO: 415) CCAAATTCTAAACCAATTTCC (SEQ ID NO: 416)15 CDH1 GAGGTTGGGGTTAGAGGAT 478 (SEQ ID NO: 15) (SEQ ID NO: 417)CAAACTCACAAATACTTTACAATTC (SEQ ID NO: 418) 16 CDKN1AGGATTAGTGGGAATAGAGGTG 408 (SEQ ID NO: 16) (SEQ ID NO: 419)AAACCCAAACTCCTAACTACC (SEQ ID NO: 420) 17 CDKN1B GTGGGGAGGTAGTTGAAGA 478(p27? Kip1) (SEQ ID NO: 421) (SEQ ID NO: 17) ATACACCCCTAACCCAAAAT(SEQ ID NO: 422) 18 CDKN2a TTGAAAATTAAGGGTTGAGG 598 (SEQ ID NO: 18)(SEQ ID NO: 423) CACCCTCTAATAACCAACCA (SEQ ID NO: 424) 19 CDKN2aGGGGTTGGTTGGTTATTAGA 256 (SEQ ID NO: 18) (SEQ ID NO: 425)AACCCTCTACCCACCTAAAT (SEQ ID NO: 426) 20 CDKN2B GGTTGGTTGAAGGAATAGAAAT708 (SEQ ID NO: 19) (SEQ ID NO: 427) CCCACTAAACATACCCTTATTC(SEQ ID NO: 428) 21 CD44 GAAAGGAGAGGTTAAAGGTTG 696 (SEQ ID NO: 20)(SEQ ID NO: 429) AACTCACTTAACTCCAATCCC (SEQ ID NO: 430) 22 CSPG2GGATAGGAGTTGGGATTAAGAT 414 (SEQ ID NO: 21) (SEQ ID NO: 431)AAATCTTTTTCAACACCAAAAT (SEQ ID NO: 432) 23 DAPK1 AACCCTTTCTTCAAATTACAAA348 (SEQ ID NO: 22) (SEQ ID NO: 433) TGATTGGGTTTTAGGGAAATA(SEQ ID NO: 434) 24 EGFR GGGTTTGGTTGTAATATGGATT 732 (SEQ ID NO: 23)(SEQ ID NO: 435) CCCAACACTACCCCTCTAA (SEQ ID NO: 436) 25 EYA4GGAAGAGGTGATTAAATGGAT 226 (SEQ ID NO: 24) (SEQ ID NO: 437)CCCAAAAATCAAACAACAA (SEQ ID NO: 438) 26 GSTP1 ATTTGGGAAAGAGGGAAAG 300(SEQ ID NO: 25) (SEQ ID NO: 439) TAAAAACTCTAAACCCCATCC (SEQ ID NO: 440)27 GTBP/MSH6 CCCTACCCACCAATATACC 278 (SEQ ID NO: 26) (SEQ ID NO: 441)AGATTTGGGGAAGAAGTTGTA (SEQ ID NO: 442) 28 HIC-1 TGGGTTGGAGAAGAAGTTTA 280(SEQ ID NO: 27) (SEQ ID NO: 443) TCATATTTCCAAAAACACACC (SEQ ID NO: 444)29 HRAS CTTATTCCCATCTAAACCCTATT 331 (SEQ ID NO: 28) (SEQ ID NO: 445)GTGGTTTTGTGAAGTTTTAGGT (SEQ ID NO: 446) 30 IGF2 CCCTTCCCCTTAACTAAACT 364(SEQ ID NO: 29) (SEQ ID NO: 447) AATTTGGGTTAGGTTTGGA (SEQ ID NO: 448) 31LKB1 TAAAAGAAGGATTTTTGATTGG 528 (SEQ ID NO: 30) (SEQ ID NO: 449)CATCTTATTTACCTCCCTCCC (SEQ ID NO: 450) 32 MGMT AAGGTTTTAGGGAAGAGTGTTT636 (SEQ ID NO: 31) (SEQ ID NO: 451) ACCTTTTCCTATCACAAAAATAA(SEQ ID NO: 452) 33 MLH1 TAAGGGGAGAGGAGGAGTTT 545 (SEQ ID NO: 32)(SEQ ID NO: 453) ACCAATTCTCAATCATCTCTTT (SEQ ID NO: 454) 34 MNCA9GGGAAGTAGGTTAGGGTTAGTT 616 (SEQ ID NO: 33) (SEQ ID NO: 455)AAATCCTCCTCTCCAAATAAAT (SEQ ID NO: 456) 35 MSH3 TGTTTGGGATTGGGTAGG 211(SEQ ID NO: 34) (SEQ ID NO: 457) CATAACCTTTACCTATCTCCTCA(SEQ ID NO: 458) 36 MYC GAGAGGGAGTAAAAGAAAATGGT 712 (SEQ ID NO: 35)(SEQ ID NO: 459) CCAAATAAACAAAATAACCTCC (SEQ ID NO: 460) 37 N33TTTTAGATTGAGGTTTTAGGGT 497 (SEQ ID NO: 36) (SEQ ID NO: 461)ATCCATTCTACCTCCTTTTTCT (SEQ ID NO: 462) 38 PAX6 GGAGGGGAGAGGGTTATG 374(SEQ ID NO: 37) (SEQ ID NO: 463) TACTATACACACCCCAAAACAA (SEQ ID NO: 464)39 PGR TTTGGGAATGGGTTGTAT 369 (SEQ ID NO: 38) (SEQ ID NO: 465)CTACCCTTAACCTCCATCCTA (SEQ ID NO: 466) 40 PTENTTTTAGGTAGTTATATTGGGTATGTT 346 (SEQ ID NO: 39) (SEQ ID NO: 467)TCAACTCTCAAACTTCCATCA (SEQ ID NO: 468) 41 RARB TTGTTGGGAGTTTTTAAGTTTT353 (SEQ ID NO: 40) (SEQ ID NO: 469) CAAATTCTCCTTCCAAATAAAT(SEQ ID NO: 470) 42 SFN GAAGAGAGGAGAGGGAGGTA 489 (SEQ ID NO: 41)(SEQ ID NO: 471) CTATCCAACAAACCCAACA (SEQ ID NO: 472) 43 S100A2GTTTTTAAGTTGGAGAAGAGGA 460 (SEQ ID NO: 42) (SEQ ID NO: 473)ACCTATAAATCACAACCCACTC (SEQ ID NO: 474) 44 TGFBR2 GTAATTTGAAGAAAGTTGAGGG296 (SEQ ID NO: 43) (SEQ ID NO: 475) CCAACAACTAAACAAAACCTCT(SEQ ID NO: 476) 45 TIMP3 TGAGAAAATTGTTGTTTGAAGT 306 (SEQ ID NO: 44)(SEQ ID NO: 477) CAAAATACCCTAAAAACCACTC (SEQ ID NO: 478) 46 TP53GGAGTTGTATTGTTGGGAGA 279 (SEQ ID NO: 45) (SEQ ID NO: 479)TAAAACCCCAATTTTCACTAA (SEQ ID NO: 480) 47 TP73 AGTAAATAGTGGGTGAGTTATGAA607 (SEQ ID NO: 46) (SEQ ID NO: 481) GAAAAACCTCTAAAAACTACTCTCC(SEQ ID NO: 482) 48 VHL TGTAAAATGAATAAAGTTAATGAGTG 362 (SEQ ID NO: 47)(SEQ ID NO: 483) TCCTAAATTCAAATAATCCTCCT (SEQ ID NO: 484) 49 CDKN1CGGGGAGGTAGATATTTGGATAA 300 (SEQ ID NO: 48) (SEQ ID NO: 485)AACTACACCATTTATATTCCCAC (SEQ ID NO: 486) 50 CAV1 GTTAGTATGTTTGGGGGTAAAT435 (SEQ ID NO: 49) (SEQ ID NO: 487) ATAAATAACACCTTCCACCCTA(SEQ ID NO: 488) 51 CDH13 TTGTATTAGGTTGGAAGTGGT 286 (SEQ ID NO: 50)(SEQ ID NO: 489) CCCAAATAAATCAACAACAACA (SEQ ID NO: 490) 52 DRG1GGTTTTGGGTTTAGTGGTAAAT 416 (SEQ ID NO: 51) (SEQ ID NO: 491)AACTTTCATAACTCACCCTTTC (SEQ ID NO: 492) 53 PTGS2 GATTTTTGGAGAGGAAGTTAAG381 (SEQ ID NO: 52) (SEQ ID NO: 493) AAAACTAAAAACCAAACCCATA(SEQ ID NO: 494) 54 THBS1 TGGGGTTAGTTTAGGATAGG 398 (SEQ ID NO: 53)(SEQ ID NO: 495) CTTAAAAACACTAAAACTTCTCAAA (SEQ ID NO: 496) 55 TPEFTTGTTTGGGTTAATAAATGGA 295 (= TMEFF2; = HPP1) (SEQ ID NO: 497)(SEQ ID NO: 54) CTTCTCTCTTCTCCCCTCTC (SEQ ID NO: 498) 56 DNMT1TCCCCATCACACCTAAAA 210 (SEQ ID NO: 55) (SEQ ID NO: 499)GGGAGGAGGGGATGTATT (SEQ ID NO: 500) 57 CEA TATGGGAGGAGGTTAGTAAGTG 680(SEQ ID NO: 56) (SEQ ID NO: 501) CCCCAAATCCTACATATAAAAA (SEQ ID NO: 502)58 MB GTTTTTGGTAAAGGGGTAGAA 598 (SEQ ID NO: 57) (SEQ ID NO: 503)CCTAAAATATCAACCTCCACCT (SEQ ID NO: 504) 59 PCNA TTTTTAGGTTGTAAGGAGGTTTT608 (SEQ ID NO: 58) (SEQ ID NO: 505) TAAATACCTCCAACACCTTTCT(SEQ ID NO: 506) 60 CDC2 ATTAGAAGTGAAAGTAATGGAATTT 418 (SEQ ID NO: 59)(SEQ ID NO: 507) TCAATTTCCAAAAACCAAC (SEQ ID NO: 508) 61 ESR1AGGGGGAATTAAATAGAAAGAG 662 (SEQ ID NO: 60) (SEQ ID NO: 509)CAATAAAACCATCCCAAATACT (SEQ ID NO: 510) 62 CASP8 AGTGGATTTGGAGTTTAGATGT431 (SEQ ID NO: 61) (SEQ ID NO: 511) AACAAAATAAAAACTTCTCCCA(SEQ ID NO: 512) 63 RASSF1 ACCTCTCTACAAATTACAAATTCA 347 (SEQ ID NO: 62)(SEQ ID NO: 513) AGTTTGGGTTAGTTTGGGTT (SEQ ID NO: 514) 64 MSH4AGGATGTTGAGGTTTGAGATT 339 (SEQ ID NO: 63) (SEQ ID NO: 515)CACTATAATAACCACCACCCA (SEQ ID NO: 516) 65 MSHS TATTAGGAATAAAGTTGGGGAG395 (SEQ ID NO: 64) (SEQ ID NO: 517) AACCCTTCAAACAAAAATAAAA(SEQ ID NO: 518)

TABLE 2 Hybridisation oligonucleotides No: Gene Oligo: 1 MDR1TTGGTGGTCGTTTTAAGG (SEQ ID NO: 1) (SEQ ID NO: 519) 2 MDR1TTGGTGGTTGTTTTAAGG (SEQ ID NO: 1) (SEQ ID NO: 520) 3 MDR1TTGAAAGACGTGTTTATA (SEQ ID NO: 1) (SEQ ID NO: 521) 4 MDR1TTGAAAGATGTGTTTATA (SEQ ID NO: 1) (SEQ ID NO: 522) 5 MDR1AGGTGTAACGGAAGTTAG (SEQ ID NO: 1) (SEQ ID NO: 523) 6 MDR1AGGTGTAATGGAAGTTAG (SEQ ID NO: 1) (SEQ ID NO: 524) 7 MDR1TAGTTTTTCGAGGAATTA (SEQ ID NO: 1) (SEQ ID NO: 525) 8 MDR1TAGTTTTTTGAGGAATTA (SEQ ID NO: 1) (SEQ ID NO: 526) 9 APOC2GAGAGTTTCGTTTTTGTT (SEQ ID NO: 2) (SEQ ID NO: 527) 10 APOC2GAGAGTTTTGTTTTTGTT (SEQ ID NO: 2) (SEQ ID NO: 528) 11 APOC2TTGGGGGACGTTATTGTT (SEQ ID NO: 2) (SEQ ID NO: 529) 12 APOC2TTGGGGGATGTTATTGTT (SEQ ID NO: 2) (SEQ ID NO: 530) 13 APOC2TGTGTTCGTTCGGAGTTG (SEQ ID NO: 2) (SEQ ID NO: 531) 14 APOC2TGTGTTTGTTTGGAGTTG (SEQ ID NO: 2) (SEQ ID NO: 532) 15 APOC2TGGGTTTGCGGAGAATGG (SEQ ID NO: 2) (SEQ ID NO: 533) 16 APOC2TGGGTTTGTGGAGAATGG (SEQ ID NO: 2) (SEQ ID NO: 534) 17 CACNA1GTTTAGGAGCGTTAATGTG (SEQ ID NO: 3) (SEQ ID NO: 535) 18 CACNA1GTTTAGGAGTGTTAATGTG (SEQ ID NO: 3) (SEQ ID NO: 536) 19 CACNA1GTAGGGTTACGAGGTTAGG (SEQ ID NO: 3) (SEQ ID NO: 537) 20 CACNA1GTAGGGTTATGAGGTTAGG (SEQ ID NO: 3) (SEQ ID NO: 538) 21 CACNA1GGGAGGTTACGTTTAGATT (SEQ ID NO: 3) (SEQ ID NO: 539) 22 CACNA1GGGAGGTTATGTTTAGATT (SEQ ID NO: 3) (SEQ ID NO: 540) 23 CACNA1GTTAGGGGTCGTGGATAAA (SEQ ID NO: 3) (SEQ ID NO: 541) 24 CACNA1GTTAGGGGTTGTGGATAAA (SEQ ID NO: 3) (SEQ ID NO: 542) 25 EGR4GGTGGGAAGCGTATTTAT (SEQ ID NO: 4) (SEQ ID NO: 543) 26 EGR4GGTGGGAAGTGTATTTAT (SEQ ID NO: 4) (SEQ ID NO: 544) 27 EGR4TTATAGTTCGAGTTTTTT (SEQ ID NO: 4) (SEQ ID NO: 545) 28 EGR4TTATAGTTTGAGTTTTTT (SEQ ID NO: 4) (SEQ ID NO: 546) 29 EGR4GGAGTTTTCGGTATATAT (SEQ ID NO: 4) (SEQ ID NO: 927) 30 EGR4GGAGTTTTTGGTATATAT (SEQ ID NO: 4) (SEQ ID NO: 928) 31 ARTGTTATTTCGAGAGAGGT (SEQ ID NO: 5) (SEQ ID NO: 547) 32 ARTGTTATTTTGAGAGAGGT (SEQ ID NO: 5) (SEQ ID NO: 548) 33 ARAGAGGTTGCGTTTTAGAG (SEQ ID NO: 5) (SEQ ID NO: 1027) 34 ARAGAGGTTGTGTTTTAGAG (SEQ ID NO: 5) (SEQ ID NO: 1028) 35 ARATTTTGAGCGAGGTTAGT (SEQ ID NO: 5) (SEQ ID NO: 549) 36 ARATTTTGAGTGAGGTTAGT (SEQ ID NO: 5) (SEQ ID NO: 550) 37 ARGTAGTATTCGAAGGTAGT (SEQ ID NO: 5) (SEQ ID NO: 551) 38 ARGTAGTATTTGAAGGTAGT (SEQ ID NO: 5) (SEQ ID NO: 552) 39 RB1TTAGATTTCGGGATAGGG (SEQ ID NO: 6) (SEQ ID NO: 553) 40 RB1TTAGATTTTGGGATAGGG (SEQ ID NO: 6) (SEQ ID NO: 554) 41 RB1TATAGTTTCGTTAAGTGT (SEQ ID NO: 6) (SEQ ID NO: 555) 42 RB1TATAGTTTTGTTAAGTGT (SEQ ID NO: 6) (SEQ ID NO: 556) 43 RB1GTGTATTTCGGTTTGGAG (SEQ ID NO: 6) (SEQ ID NO: 557) 44 RB1GTGTATTTTGGTTTGGAG (SEQ ID NO: 6) (SEQ ID NO: 558) 45 RB1TGGATTTACGTTAGGTTT (SEQ ID NO: 6) (SEQ ID NO: 559) 46 RB1TGGATTTATGTTAGGTTT (SEQ ID NO: 6) (SEQ ID NO: 560) 47 GPIb betaTGTTATTTGTCGTTGTAG (SEQ ID NO: 7) (SEQ ID NO: 561) 48 GPIb betaTGTTATTTGTTGTTGTAG (SEQ ID NO: 7) (SEQ ID NO: 562) 49 GPIb betaGTGGGAGCGGAAGTTTGA (SEQ ID NO: 7) (SEQ ID NO: 563) 50 GPIb betaGTGGGAGTGGAAGTTTGA (SEQ ID NO: 7) (SEQ ID NO: 564) 51 GPIb betaTAGAGTAAGTCGGGTTGT (SEQ ID NO: 7) (SEQ ID NO: 565) 52 GPIb betaTAGAGTAAGTCGGGTTGTT (SEQ ID NO: 7) (SEQ ID NO: 566) 53 GPIb betaGGTTAGGTCGTAGTATTG (SEQ ID NO: 7) (SEQ ID NO: 567) 54 GPIb betaGGTTAGGTTGTAGTATTG (SEQ ID NO: 7) (SEQ ID NO: 568) 55 GPIb betaGGAGTTCGGTCGGGTTTT (SEQ ID NO: 7) (SEQ ID NO: 1005) 56 GPIb betaGGAGTTTGGTTGGGTTTT (SEQ ID NO: 7) (SEQ ID NO: 1006) 57 MYOD1ATAGTAGTCGGGTGTTGG (SEQ ID NO: 8) (SEQ ID NO: 569) 58 MYOD1ATAGTAGTTGGGTGTTGG (SEQ ID NO: 8) (SEQ ID NO: 570) 59 MYOD1GTGTTAGTCGTTTAGGGT (SEQ ID NO: 8) (SEQ ID NO: 1009) 60 MYOD1GTGTTAGTTGTTTAGGGT (SEQ ID NO: 8) (SEQ ID NO: 1010) 61 MYOD1TAGTTGTTCGTTTGGGTT (SEQ ID NO: 8) (SEQ ID NO: 571) 62 MYOD1TAGTTGTTTGTTTGGGTT (SEQ ID NO: 8) (SEQ ID NO: 572) 63 MYOD1AATTAGGTCGGATAGGAG (SEQ ID NO: 8) (SEQ ID NO: 975) 64 MYOD1AATTAGGTTGGATAGGAG (SEQ ID NO: 8) (SEQ ID NO: 976) 65 WT1TAGTGAGACGAGGTTTTT (SEQ ID NO: 9) (SEQ ID NO: 1017) 66 WT1TAGTGAGATGAGGTTTTT (SEQ ID NO: 9) (SEQ ID NO: 1018) 67 WT1TATATTGGCGAAGGTTAA (SEQ ID NO: 9) (SEQ ID NO: 967) 68 WT1TATATTGGTGAAGGTTAA (SEQ ID NO: 9) (SEQ ID NO: 968) 69 WT1TGTTATATCGGTTAGTTG (SEQ ID NO: 9) (SEQ ID NO: 959) 70 WT1TGTTATATTGGTTAGTTG (SEQ ID NO: 9) (SEQ ID NO: 960) 71 WT1TTTAGTTTCGATTTTTGG (SEQ ID NO: 9) (SEQ ID NO: 573) 72 WT1TTTAGTTTTGATTTTTGG (SEQ ID NO: 9) (SEQ ID NO: 574) 73 HLA-FATAGGGTACGTTAAGGTT (SEQ ID NO: 10) (SEQ ID NO: 575) 74 HLA-FATAGGGTATGTTAAGGTT (SEQ ID NO: 10) (SEQ ID NO: 576) 75 HLA-FTATTTGGGCGGGTGAGTG (SEQ ID NO: 10) (SEQ ID NO: 939) 76 HLA-FTATTTGGGTGGGTGAGTG (SEQ ID NO: 10) (SEQ ID NO: 940) 77 HLA-FGAGAGAAACGGTTTTTGT (SEQ ID NO: 10) (SEQ ID NO: 577) 78 HLA-FGAGAGAAATGGTTTTTGT (SEQ ID NO: 10) (SEQ ID NO: 578) 79 HLA-FAGTTGTTTCGTAGATATT (SEQ ID NO: 10) (SEQ ID NO: 989) 80 HLA-FAGTTGTTTTGTAGATATT (SEQ ID NO: 10) (SEQ ID NO: 990) 81 ELK1TGTTTAATCGTAGAGTTG (SEQ ID NO: 11) (SEQ ID NO: 579) 82 ELK1TGTTTAATTGTAGAGTTG (SEQ ID NO: 11) (SEQ ID NO: 580) 83 ELK1TTTGTTTTCGTTGAGTAG (SEQ ID NO: 11) (SEQ ID NO: 581) 84 ELK1TTTGTTTTTGTTGAGTAG (SEQ ID NO: 11) (SEQ ID NO: 582) 85 ELK1GAAGGGTTCGTTTTTTAA (SEQ ID NO: 11) (SEQ ID NO: 583) 86 ELK1GAAGGGTTTGTTTTTTAA (SEQ ID NO: 11) (SEQ ID NO: 584) 87 ELK1ATTAATAGCGTTTTGGTT (SEQ ID NO: 11) (SEQ ID NO: 585) 88 ELK1ATTAATAGTGTTTTGGTT (SEQ ID NO: 11) (SEQ ID NO: 586) 89 APCTTTAATCGTATAGTTTGT (SEQ ID NO: 12) (SEQ ID NO: 971) 90 APCTTTAATTGTATAGTTTGT (SEQ ID NO: 12) (SEQ ID NO: 972) 91 APCTATTTAGCGGATTATATA (SEQ ID NO: 12) (SEQ ID NO: 587) 92 APCTATTTAGTGGATTATATA (SEQ ID NO: 12) (SEQ ID NO: 588) 93 APCTATTTTGGCGGGTTGTAT (SEQ ID NO: 12) (SEQ ID NO: 985) 94 APCTATTTTGGTGGGTTGTAT (SEQ ID NO: 12) (SEQ ID NO: 986) 95 APCAAGGTTATCGGTTTAAGA (SEQ ID NO: 12) (SEQ ID NO: 589) 96 APCAAGGTTATTGGTTTAAGA (SEQ ID NO: 12) (SEQ ID NO: 590) 97 APCGGGGGACGACGTTTTTGT (SEQ ID NO: 12) (SEQ ID NO: 591) 98 APCGGGGGATGATGTTTTTGT (SEQ ID NO: 12) (SEQ ID NO: 592) 99 BCL2AGTGTTTCGCGTGATTGA (SEQ ID NO: 13) (SEQ ID NO: 593) 100 BCL2AGTGTTTCGCGTGATTGA (SEQ ID NO: 13) (SEQ ID NO: 594) 101 BCL2TAAGTTGTCGTAGAGGGG (SEQ ID NO: 13) (SEQ ID NO: 595) 102 BCL2TAAGTTGTTGTAGAGGGG (SEQ ID NO: 13) (SEQ ID NO: 596) 103 BCL2GGATTTCGTCGTTGTAGA (SEQ ID NO: 13) (SEQ ID NO: 597) 104 BCL2GGATTTTGTTGTTGTAGA (SEQ ID NO: 13) (SEQ ID NO: 598) 105 BCL2TTTTGTTACGGTGGTGGA (SEQ ID NO: 13) (SEQ ID NO: 1025) 106 BCL2TTTTGTTATGGTGGTGGA (SEQ ID NO: 13) (SEQ ID NO: 1026) 107 CALCAGAGGGTGACGTAATTTAG (SEQ ID NO: 14) (SEQ ID NO: 599) 108 CALCAGAGGGTGATGTAATTTAG (SEQ ID NO: 14) (SEQ ID NO: 600) 109 CALCATGTATTGGCGGAATTTTT (SEQ ID NO: 14) (SEQ ID NO: 601) 110 CALCATGTATTGGTGGAATTTTT (SEQ ID NO: 14) (SEQ ID NO: 602) 111 CALCAATTAGGTTCGTGTTTTAG (SEQ ID NO: 14) (SEQ ID NO: 953) 112 CALCAATTAGGTTTGTGTTTTAG (SEQ ID NO: 14) (SEQ ID NO: 954) 113 CALCAGTTAGTTTCGGGATATTT (SEQ ID NO: 14) (SEQ ID NO: 603) 114 CALCAGTTAGTTTTGGGATATTT (SEQ ID NO: 14) (SEQ ID NO: 604) 115 CDH1TAGAGGATCGTTTGAGTT (SEQ ID NO: 15) (SEQ ID NO: 605) 116 CDH1TAGAGGATTGTTTGAGTT (SEQ ID NO: 15) (SEQ ID NO: 606) 117 CDH1GTTGTGATCGTATTATTG (SEQ ID NO: 15) (SEQ ID NO: 607) 118 CDH1GTTGTGATTGTATTATTG (SEQ ID NO: 15) (SEQ ID NO: 608) 119 CDH1TTGGGATTCGAATTTAGT (SEQ ID NO: 15) (SEQ ID NO: 609) 120 CDH1TTGGGATTTGAATTTAGT (SEQ ID NO: 15) (SEQ ID NO: 610) 121 CDH1AGGGTTATCGCGTTTATG (SEQ ID NO: 15) (SEQ ID NO: 983) 122 CDH1AGGGTTATTGTGTTTATG (SEQ ID NO: 15) (SEQ ID NO: 984) 123 CDH1TAGTGGCGTCGGAATTGT (SEQ ID NO: 15) (SEQ ID NO: 929) 124 CDH1TAGTGGTGTTGGAATTGT (SEQ ID NO: 15) (SEQ ID NO: 930) 125 CDKN1AAGGTGTATCGTTTTTATA (SEQ ID NO: 16) (SEQ ID NO: 611) 126 CDKN1AAGGTGTATTGTTTTTATA (SEQ ID NO: 16) (SEQ ID NO: 612) 127 CDKN1ATGGGTTAGCGGTGAGTTA (SEQ ID NO: 16) (SEQ ID NO: 613) 128 CDKN1ATGGGTTAGTGGTGAGTTA (SEQ ID NO: 16) (SEQ ID NO: 614) 129 CDKN1AGTTTATTTCGTGGGGAAA (SEQ ID NO: 16) (SEQ ID NO: 615) 130 CDKN1AGTTTATTTTGTGGGGAAA (SEQ ID NO: 16) (SEQ ID NO: 616) 131 CDKN1ATTGGAATTCGGTTAGGTT (SEQ ID NO: 16) (SEQ ID NO: 617) 132 CDKN1ATTGGAATTTGGTTAGGTT (SEQ ID NO: 16) (SEQ ID NO: 618) 133 CDKN1BAAGAGAAACGTTGGAATA (p27 Kip1) (SEQ ID NO: 619) (SEQ ID NO: 17) 134CDKN1B AAGAGAAATGTTGGAATA (p27 Kip1) (SEQ ID NO: 620) (SEQ ID NO: 17)135 CDKN1B TTTGATTTCGAGGGGAGT (p27 Kip1) (SEQ ID NO: 621)(SEQ ID NO: 17) 136 CDKN1B TTTGATTTTGAGGGGAGT (p27 Kip1)(SEQ ID NO: 622) (SEQ ID NO: 17) 137 CDKN1B GTATTTGGCGGTTGGATT(p27 Kip1) (SEQ ID NO: 623) (SEQ ID NO: 17) 138 CDKN1BGTATTTGGTGGTTGGATT (p27 Kip1) (SEQ ID NO: 624) (SEQ ID NO: 17) 139CDKN1B TATAATTTCGGGAAAGAA (p27 Kip1) (SEQ ID NO: 625) (SEQ ID NO: 17)140 CDKN1B TATAATTTTGGGAAAGAA (p27 Kip1) (SEQ ID NO: 626)(SEQ ID NO: 17) 141 CDKN2a AGAGTGAACGTATTTAAA (SEQ ID NO: 18)(SEQ ID NO: 627) 142 CDKN2a AGAGTGAATGTATTTAAA (SEQ ID NO: 18)(SEQ ID NO: 628) 143 CDKN2a GTTGTTTTCGGTTGGTGT (SEQ ID NO: 18)(SEQ ID NO: 1029) 144 CDKN2a GTTGTTTTTGGTTGGTGT (SEQ ID NO: 18)(SEQ ID NO: 1030) 145 CDKN2a GATAGGGTCGGAGGGGGT (SEQ ID NO: 18)(SEQ ID NO: 629) 146 CDKN2a GATAGGGTTGGAGGGGGT (SEQ ID NO: 18)(SEQ ID NO: 630) 147 CDKN2a GGAGTTTTCGGTTGATTG (SEQ ID NO: 18)(SEQ ID NO: 997) 148 CDKN2a GGAGTTTTTGGTTGATTG (SEQ ID NO: 18)(SEQ ID NO: 998) 149 CDKN2a AATAGTTACGGTCGGAGG (SEQ ID NO: 18)(SEQ ID NO: 981) 150 CDKN2a AATAGTTATGGTTGGAGG (SEQ ID NO: 18)(SEQ ID NO: 982) 151 CDKN2B ATATTTAGCGAGTAGTGT (SEQ ID NO: 19)(SEQ ID NO: 631) 152 CDKN2B ATATTTAGTGAGTAGTGT (SEQ ID NO: 19)(SEQ ID NO: 632) 153 CDKN2B ATAGGGGGCGGAGTTTAA (SEQ ID NO: 19)(SEQ ID NO: 633) 154 CDKN2B ATAGGGGGTGGAGTTTAA (SEQ ID NO: 19)(SEQ ID NO: 634) 155 CDKN2B TTATTGTACGGGGTTTTA (SEQ ID NO: 19)(SEQ ID NO: 635) 156 CDKN2B TTATTGTATGGGGTTTTA (SEQ ID NO: 19)(SEQ ID NO: 636) 157 CDKN2B TTTTAAGTCGTAGAAGGA (SEQ ID NO: 19)(SEQ ID NO: 637) 158 CDKN2B TTTTAAGTTGTAGAAGGA (SEQ ID NO: 19)(SEQ ID NO: 638) 159 CD44 GTGGGGTTCGGAGGTATA (SEQ ID NO: 20)(SEQ ID NO: 919) 160 CD44 GTGGGGTTCGGAGGTATA (SEQ ID NO: 20)(SEQ ID NO: 920) 161 CD44 GGTAGTTTCGATTATTTA (SEQ ID NO: 20)(SEQ ID NO: 639) 162 CD44 GGTAGTTTCGATTATTTA (SEQ ID NO: 20)(SEQ ID NO: 640) 163 CD44 TTGTTTAGCGGATTTTAG (SEQ ID NO: 20)(SEQ ID NO: 897) 164 CD44 TCGTTTAGTGGATTTTAG (SEQ ID NO: 20)(SEQ ID NO: 898) 165 CD44 TGGTGGTACGTAGTTTGG (SEQ ID NO: 20)(SEQ ID NO: 641) 166 CD44 TGGTGGTATGTAGTTTGG (SEQ ID NO: 20)(SEQ ID NO: 642) 167 CSPG2 AAGATTTTCGGTTAGTTT (SEQ ID NO: 21)(SEQ ID NO: 963) 168 CSPG2 AAGATTTTTGGTTAGTTT (SEQ ID NO: 21)(SEQ ID NO: 964) 169 CSPG2 ATGTGATTCGTTTGGGTA (SEQ ID NO: 21)(SEQ ID NO: 643) 170 CSPG2 ATGTGATTCGTTTGGGTA (SEQ ID NO: 21)(SEQ ID NO: 644) 171 CSPG2 GGGTAACGTCGAATTCAG (SEQ ID NO: 21)(SEQ ID NO: 901) 172 CSPG2 GGGTAATGTTGAATTTAG (SEQ ID NO: 21)(SEQ ID NO: 902) 173 CSPG2 AAAAATTCGCGAGTCTAG (SEQ ID NO: 21)(SEQ ID NO: 945) 174 CSPG2 AAAAATTTGTGAGTTCAG (SEQ ID NO: 21)(SEQ ID NO: 946) 175 DAPK1 GTTGGAGTCGAGGTTCGA (SEQ ID NO: 22)(SEQ ID NO: 645) 176 DAPK1 GTTGGAGTCGAGGTTCGA (SEQ ID NO: 22)(SEQ ID NO: 646) 177 DAPK1 TTTTCTGTCGGATTGGTG (SEQ ID NO: 22)(SEQ ID NO: 647) 178 DAPK1 TTTTTCGTTGGATTGGTG (SEQ ID NO: 22)(SEQ ID NO: 648) 179 DAPK1 GAAGGGAGCGTATTTCAT (SEQ ID NO: 22)(SEQ ID NO: 955) 180 DAPK1 GAAGGGAGTGTATTTTAT (SEQ ID NO: 22)(SEQ ID NO: 956) 181 DAPK1 TTGTTTTTCGGAAATTTG (SEQ ID NO: 22)(SEQ ID NO: 935) 182 DAPK1 TTGTTTTTTGGAAATTTG (SEQ ID NO: 22)(SEQ ID NO: 936) 183 EGFR TTTGTATTCGGAGTTGGG (SEQ ID NO: 23)(SEQ ID NO: 961) 184 EGFR TTTGTATTTGGAGTTGGG (SEQ ID NO: 23)(SEQ ID NO: 962) 185 EGFR GATGATTTCGAGGGTGTT (SEQ ID NO: 23)(SEQ ID NO: 649) 186 EGFR GATGATTTTGAGGGTGTT (SEQ ID NO: 23)(SEQ ID NO: 650) 187 EGFR GAGGGTTTCGTAGTGTTG (SEQ ID NO: 23)(SEQ ID NO: 651) 188 EGFR GAGGGTTTTGTAGTGTTG (SEQ ID NO: 23)(SEQ ID NO: 652) 189 EGFR TGGGGATTCGAATAAAGG (SEQ ID NO: 23)(SEQ ID NO: 653) 190 EGFR TGGGGATTTGAATAAAGG (SEQ ID NO: 23)(SEQ ID NO: 654) 191 EGFR ATTTGGTTCGATTTGGAT (SEQ ID NO: 23)(SEQ ID NO: 931) 192 EGFR ATTTGGTTTGATTTGGAT (SEQ ID NO: 23)(SEQ ID NO: 932) 193 EYA4 TATATATACGTGTGGGTA (SEQ ID NO: 24)(SEQ ID NO: 655) 194 EYA4 TATATATATGTGTGGGTA (SEQ ID NO: 24)(SEQ ID NO: 656) 195 EYA4 AGTGTATGCGTAGAAGGT (SEQ ID NO: 24)(SEQ ID NO: 923) 196 EYA4 AGTGTATGTGTAGAAGGT (SEQ ID NO: 24)(SEQ ID NO: 924) 197 EYA4 TTTAGATACGAAATGTTA (SEQ ID NO: 24)(SEQ ID NO: 657) 198 EYA4 TTTAGATATGAAATGTTA (SEQ ID NO: 24)(SEQ ID NO: 658) 199 EYA4 AAGTAAGTCGTTGTTGTT (SEQ ID NO: 24)(SEQ ID NO: 921) 200 EYA4 AAGTAAGTTGTTGTTGTT (SEQ ID NO: 24)(SEQ ID NO: 922) 201 GSTP1 GGTTTTTTCGGTTAGTTG (SEQ ID NO: 25)(SEQ ID NO: 659) 202 GSTP1 GGTFTTITTGGTTAGTTG (SEQ ID NO: 25)(SEQ ID NO: 660) 203 GSTP1 GGAGTTCGCGGGATTFTT (SEQ ID NO: 25)(SEQ ID NO: 905) 204 GSTP1 GGAGTTTGTGGGATTTTT (SEQ ID NO: 25)(SEQ ID NO: 906) 205 GSTP1 GTAGTFTTCGTTATTAGT (SEQ ID NO: 25)(SEQ ID NO: 661) 206 GSTP1 GTAGTTFTTGITATTAGT (SEQ ID NO: 25)(SEQ ID NO: 662) 207 GTBP/MSH6 GAGGAATTCGGGTTTTAG (SEQ ID NO: 26)(SEQ ID NO: 951) 208 GTBP/MSH6 GAGGAATTTGGGTTTTAG (SEQ ID NO: 26)(SEQ ID NO: 952) 209 GTBP/MSH6 TTTGTTGGCGGGAAATTT (SEQ ID NO: 26)(SEQ ID NO: 925) 210 GTBP/MSH6 ITTUFTGGTGGGAAATIT (SEQ ID NO: 26)(SEQ ID NO: 926) 211 GTBP/MSH6 TTTTGTCGGACGGAGTTT (SEQ ID NO: 26)(SEQ ID NO: 663) 212 GTBP/MSH6 TTFTGTTGGATGGAGTFT (SEQ ID NO: 26)(SEQ ID NO: 664) 213 GTBP/MSH6 AAGGTTTAATCGTTTTGT (SEQ ID NO: 26)(SEQ ID NO: 665) 214 GTBP/MSH6 AAGGTTTAATTGTTTTGT (SEQ ID NO: 26)(SEQ ID NO: 666) 215 HIC-1 TTAAAACGGCGTATAGGG (SEQ ID NO: 27)(SEQ ID NO: 667) 216 HIC-1 TTAAAATGGTGTATAGGG (SEQ ID NO: 27)(SEQ ID NO: 668) 217 HIC-1 AGGAGATTCGAAAGTTTA (SEQ ID NO: 27)(SEQ ID NO: 669) 218 HIC-1 AGGAGATTTGAAAGTTTA (SEQ ID NO: 27)(SEQ ID NO: 670) 219 HIC-1 TTTTAGAGCGTTAGGGTT (SEQ ID NO: 27)(SEQ ID NO: 1021) 220 HIC-1 TTTTAGAGTGTTAGGGTT (SEQ ID NO: 27)(SEQ ID NO: 1022) 221 HRAS ATAGTGGGCGTAATTGGT (SEQ ID NO: 28)(SEQ ID NO: 671) 222 HRAS ATAGTGGGTGTAATTGGT (SEQ ID NO: 28)(SEQ ID NO: 672) 223 HRAS AAATTGGACGTTTAGTTG (SEQ ID NO: 28)(SEQ ID NO: 673) 224 HRAS AAATTGGATGTTTAGTTG (SEQ ID NO: 28)(SEQ ID NO: 674) 225 HRAS TAGAAGTCGAGAGATTTG (SEQ ID NO: 28)(SEQ ID NO: 675) 226 HRAS TAGAAGTTGAGAGATTTG (SEQ ID NO: 28)(SEQ ID NO: 676) 227 HRAS GAATATTTCGAAGTTTGT (SEQ ID NO: 28)(SEQ ID NO: 677) 228 HRAS GAATATTTTGAAGTTTGT (SEQ ID NO: 28)(SEQ ID NO: 678) 229 IGF2 AGTTTGAACGATGTAAGA (SEQ ID NO: 29)(SEQ ID NO: 973) 230 IGF2 AGTTTGAATGATGTAAGA (SEQ ID NO: 29)(SEQ ID NO: 974) 231 IGF2 GGTTATTACGATAATTTG (SEQ ID NO: 29)(SEQ ID NO: 679) 232 IGF2 GGTTATTATGATAATTTG (SEQ ID NO: 29)(SEQ ID NO: 680) 233 IGF2 TTGTATGGTCGAGTTTAT (SEQ ID NO: 29)(SEQ ID NO: 941) 234 IGF2 TTGTATGGTTGAGTTTAT (SEQ ID NO: 29)(SEQ ID NO: 942) 235 IGF2 GATTAGGGCGGGAAATAT (SEQ ID NO: 29)(SEQ ID NO: 937) 236 IGF2 GATTAGGGTGGGAAATAT (SEQ ID NO: 29)(SEQ ID NO: 938) 237 IGF2 TGGAGTTTACGGAGGTTT (SEQ ID NO: 29)(SEQ ID NO: 681) 238 IGF2 TGGAGTTTATGGAGGTTT (SEQ ID NO: 29)(SEQ ID NO: 682) 239 LKB1 TTAATTAACGGGTGGGTA (SEQ ID NO: 30)(SEQ ID NO: 683) 240 LKB1 TTAATTAATGGGTGGGTA (SEQ ID NO: 30)(SEQ ID NO: 684) 241 LKB1 TTTAGGTTCGTAAGTTTA (SEQ ID NO: 30)(SEQ ID NO: 965) 242 LKB1 TTTAGGTTTGTAAGTTTA (SEQ ID NO: 30)(SEQ ID NO: 966) 243 LKB1 AGGGAGGTCGTTGGTATT (SEQ ID NO: 30)(SEQ ID NO: 933) 244 LKB1 AGGGAGGTTGTTGGTATT (SEQ ID NO: 30)(SEQ ID NO: 934) 245 MGMT TAAGGATACGAGTTATAT (SEQ ID NO: 31)(SEQ ID NO: 685) 246 MGMT TAAGGATATGAGTTATAT (SEQ ID NO: 31)(SEQ ID NO: 686) 247 MGMT TTGGAGAGCGGTTGAGTT (SEQ ID NO: 31)(SEQ ID NO: 687) 248 MGMT TTGGAGAGTGGTTGAGTT (SEQ ID NO: 31)(SEQ ID NO: 688) 249 MGMT TAGGTTATCGGTGATTGT (SEQ ID NO: 31)(SEQ ID NO: 689) 250 MGMT TAGGTTATTGGTGATTGT (SEQ ID NO: 31)(SEQ ID NO: 690) 251 MGMT TAGGGGAGCGGTTTTAGG (SEQ ID NO: 31)(SEQ ID NO: 691) 252 MGMT TAGGGGAGTGGTTTTAGG (SEQ ID NO: 31)(SEQ ID NO: 692) 253 MGMT AGTAGGATCGGGATTTTT (SEQ ID NO: 31)(SEQ ID NO: 1001) 254 MGMT AGTAGGATTGGGATTTTT (SEQ ID NO: 31)(SEQ ID NO: 1002) 255 MLH1 TTGAGAAGCGTTAAGTAT (SEQ ID NO: 32)(SEQ ID NO: 693) 256 MLH1 TTGAGAAGTGTTAAGTAT (SEQ ID NO: 32)(SEQ ID NO: 694) 257 MLH1 TTAGGTAGCGGGTAGTAG (SEQ ID NO: 32)(SEQ ID NO: 949) 258 MLH1 TTAGGTAGTGGGTAGTAG (SEQ ID NO: 32)(SEQ ID NO: 950) 259 MLH1 GTAGTAGTCGTTTTAGGG (SEQ ID NO: 32)(SEQ ID NO: 695) 260 MLH1 GTAGTAGTTGTTTTAGGG (SEQ ID NO: 32)(SEQ ID NO: 696) 261 MLH1 ATAGTTGTCGTTGAAGGG (SEQ ID NO: 32)(SEQ ID NO: 697) 262 MLH1 ATAGTTGTCGTTGAAGGG (SEQ ID NO: 32)(SEQ ID NO: 698) 263 MLH1 TTGGATGGCGTAAGTTAT (SEQ ID NO: 32)(SEQ ID NO: 699) 264 MLH1 TTGGATGGTGTAAGTTAT (SEQ ID NO: 32)(SEQ ID NO: 700) 265 MNCA9 TAAAAGGGCGTTTTGTGA (SEQ ID NO: 33)(SEQ ID NO: 701) 266 MNCA9 TAAAAGGGCGTTTTGTGA (SEQ ID NO: 33)(SEQ ID NO: 702) 267 MNCA9 TAGTTAGTCGTATGGTTT (SEQ ID NO: 33)(SEQ ID NO: 703) 268 MNCA9 TAGTTAGTTGTATGGTTT (SEQ ID NO: 33)(SEQ ID NO: 704) 269 MNCA9 GATTTATTCGGAGAGGAG (SEQ ID NO: 33)(SEQ ID NO: 705) 270 MNCA9 GATTTATTCGGAGAGGAG (SEQ ID NO: 33)(SEQ ID NO: 706) 271 MSH3 ATTTTTCGTTCGATGATA (SEQ ID NO: 34)(SEQ ID NO: 707) 272 MSH3 ATTTTTTGTTTGATGATA (SEQ ID NO: 34)(SEQ ID NO: 708) 273 MSH3 AGTTTAGTCGGGGTTATA (SEQ ID NO: 34)(SEQ ID NO: 709) 274 MSH3 AGTTTAGTTGGGGTTATA (SEQ ID NO: 34)(SEQ ID NO: 710) 275 MSH3 GGGTGAAGCGTTGAGGTT (SEQ ID NO: 34)(SEQ ID NO: 711) 276 MSH3 GGGTGAAGTGTTGAGGTT (SEQ ID NO: 34)(SEQ ID NO: 712) 277 MSH3 AGTATTTTCGTTTGAGGA (SEQ ID NO: 34)(SEQ ID NO: 1015) 278 MSH3 AGTATTTTTGTTTGAGGA (SEQ ID NO: 34)(SEQ ID NO: 1016) 279 MYC TTAGAGTGTTCGGTTGTT (SEQ ID NO: 35)(SEQ ID NO: 713) 280 MYC TTAGAGTGTTTGGTTGTT (SEQ ID NO: 35)(SEQ ID NO: 714) 281 MYC TTATAATGCGAGGGTTTG (SEQ ID NO: 35)(SEQ ID NO: 1019) 282 MYC TTATAATGTGAGGGTTTG (SEQ ID NO: 35)(SEQ ID NO: 1020) 283 MYC AGGATTTTCGAGTTGTGT (SEQ ID NO: 35)(SEQ ID NO: 715) 284 MYC AGGATTTTTGAGTTGTGT (SEQ ID NO: 35)(SEQ ID NO: 716) 285 MYC AATTTTAGCGAGAGGTAG (SEQ ID NO: 35)(SEQ ID NO: 717) 286 MYC AATTTTAGTGAGAGGTAG (SEQ ID NO: 35)(SEQ ID NO: 718) 287 N33 TTGGTTCGGGAAAGGTAA (SEQ ID NO: 36)(SEQ ID NO: 977) 288 N33 TTGGTTTGGGAAAGGTAA (SEQ ID NO: 36)(SEQ ID NO: 978) 289 N33 TGTTATTTCGGAGGGTTT (SEQ ID NO: 36)(SEQ ID NO: 909) 290 N33 TGTTATTTTGGAGGGTTT (SEQ ID NO: 36)(SEQ ID NO: 910) 291 N33 GTTTAGTTAGCGGGTTTT (SEQ ID NO: 36)(SEQ ID NO: 943) 292 N33 GTTTAGTTAGTGGGTTTT (SEQ ID NO: 36)(SEQ ID NO: 944) 293 N33 ATTTAGTTCGGGGGAGGA (SEQ ID NO: 36)(SEQ ID NO: 993) 294 N33 ATTTAGTTTGGGGGAGGA (SEQ ID NO: 36)(SEQ ID NO: 994) 295 PAX6 TATTGTTTCGGTTGTTAG (SEQ ID NO: 37)(SEQ ID NO: 719) 296 PAX6 TATTGTTTTGGTTGTTAG (SEQ ID NO: 37)(SEQ ID NO: 720) 297 PAX6 GTTAGTAGCGAGTTTAGG (SEQ ID NO: 37)(SEQ ID NO: 721) 298 PAX6 GTTAGTAGTGAGTTTAGG (SEQ ID NO: 37)(SEQ ID NO: 722) 299 PAX6 AGAGTTTAGCGTATTTTT (SEQ ID NO: 37)(SEQ ID NO: 723) 300 PAX6 AGAGTTTAGTGTATTTTT (SEQ ID NO: 37)(SEQ ID NO: 724) 301 PGR GAATTTAGCGAGGGATTG (SEQ ID NO: 38)(SEQ ID NO: 725) 302 PGR GAATTTAGTGAGGGATTG (SEQ ID NO: 38)(SEQ ID NO: 726) 303 PGR AGTATGTACGAGTTTGAT (SEQ ID NO: 38)(SEQ ID NO: 727) 304 PGR AGTATGTATGAGTTTGAT (SEQ ID NO: 38)(SEQ ID NO: 728) 305 PGR TTAAGTGTCGGATTTGTG (SEQ ID NO: 38)(SEQ ID NO: 1011) 306 PGR TTAAGTGTTGGATTTGTG (SEQ ID NO: 38)(SEQ ID NO: 1012) 307 PGR GGGATAAACGATAGTTAT (SEQ ID NO: 38)(SEQ ID NO: 729) 308 PGR GGGATAAATGATAGTTAT (SEQ ID NO: 38)(SEQ ID NO: 730) 309 PTEN AGAGTTTGCGGTTTGGGG (SEQ ID NO: 39)(SEQ ID NO: 731) 310 PTEN AGAGTTTGTGGTTTGGGGT (SEQ ID NO: 39)(SEQ ID NO: 732) 311 PTEN ATTTTGCGTTCGTATTTA (SEQ ID NO: 39)(SEQ ID NO: 987) 312 PTEN ATTTTGTGTTTGTATTTA (SEQ ID NO: 39)(SEQ ID NO: 988) 313 PTEN AGAGTTATCGTTTTGTTT (SEQ ID NO: 39)(SEQ ID NO: 957) 314 PTEN AGAGTTATTGTTTTGTTT (SEQ ID NO: 39)(SEQ ID NO: 958) 315 PTEN TGATGTGGCGGGATTTTT (SEQ ID NO: 39)(SEQ ID NO: 947) 316 PTEN TGATGTGGTGGGATTTTT (SEQ ID NO: 39)(SEQ ID NO: 948) 317 RARB TAGTAGTTCGGGTAGGGT (SEQ ID NO: 40)(SEQ ID NO: 991) 318 RARB TAGTAGTTTGGGTAGGGT (SEQ ID NO: 40)(SEQ ID NO: 992) 319 RARB GGGTTTATCGAAAGTTTA (SEQ ID NO: 40)(SEQ ID NO: 733) 320 RARB GGGTTTATTGAAAGTTTA (SEQ ID NO: 40)(SEQ ID NO: 734) 321 RARB AGTTTATTCGTATATATT (SEQ ID NO: 40)(SEQ ID NO: 735) 322 RARB AGTTTATTTGTATATATT (SEQ ID NO: 40)(SEQ ID NO: 736) 323 RARB TTTTTATGCGAGTTGTTT (SEQ ID NO: 40)(SEQ ID NO: 737) 324 RARB TCTTTATGTGAGTTGTTT (SEQ ID NO: 40)(SEQ ID NO: 738) 325 SFN ATAGAGTTCGGTATTGGT (SEQ ID NO: 41)(SEQ ID NO: 739) 326 SFN ATAGAGTTTGGTATTGGT (SEQ ID NO: 41)(SEQ ID NO: 740) 327 SFN GTAGGTCGAACGTTATGA (SEQ ID NO: 41)(SEQ ID NO: 741) 328 SFN GTAGGTTGAATGTTATGA (SEQ ID NO: 41)(SEQ ID NO: 742) 329 SFN AAAAGTAACGAGGAGGGT (SEQ ID NO: 41)(SEQ ID NO: 743) 330 SFN AAAAGTAATGAGGAGGGT (SEQ ID NO: 41)(SEQ ID NO: 744) 331 S100A2 TTAATTGCGGTTGTGTG (SEQ ID NO: 42)(SEQ ID NO: 745) 332 S100A2 TTTAATTGTGGTTGTGTG (SEQ ID NO: 42)(SEQ ID NO: 746) 333 S100A2 TATATAGGCGTATGTATG (SEQ ID NO: 42)(SEQ ID NO: 747) 334 S100A2 TATATAGGTGTATGTATG (SEQ ID NO: 42)(SEQ ID NO: 748) 335 S100A2 TATGTATACGAGTATTGG (SEQ ID NO: 42)(SEQ ID NO: 999) 336 S100A2 TATGTATATGAGTATTGG (SEQ ID NO: 42)(SEQ ID NO: 1000) 337 S100A2 AGTTTTAGCGTGTGTTTA (SEQ ID NO: 42)(SEQ ID NO: 749) 338 S100A2 AGTTTTAGTGTGTGTTTA (SEQ ID NO: 42)(SEQ ID NO: 750) 339 TGFBR2 ATTTGGAGCGAGGAATTT (SEQ ID NO: 43)(SEQ ID NO: 751) 340 TGFBR2 ATTTGGAGTGAGGAATTT (SEQ ID NO: 43)(SEQ ID NO: 752) 341 TGFBR2 TTGAAAGTCGGTTAAAGT (SEQ ID NO: 43)(SEQ ID NO: 753) 342 TGFBR2 TTGAAAGTTGGTTAAAGT (SEQ ID NO: 43)(SEQ ID NO: 754) 343 TGFBR2 AAAGTTTTCGGAGGGGTT (SEQ ID NO: 43)(SEQ ID NO: 907) 344 TGFBR2 AAAGTTTTTGGAGGGGTT (SEQ ID NO: 43)(SEQ ID NO: 908) 345 TGFBR2 GGTAGTTACGAGAGAGTT (SEQ ID NO: 43)(SEQ ID NO: 755) 346 TGFBR2 GGTAGTTATGAGAGAGTT (SEQ ID NO: 43)(SEQ ID NO: 756) 347 TIMP3 AGGTTTTTCGTTGGAGAA (SEQ ID NO: 44)(SEQ ID NO: 757) 348 TIMP3 AGGTTTTTTGTTGGAGAA (SEQ ID NO: 44)(SEQ ID NO: 758) 349 TIMP3 GAAAATATCGGTATTTTG (SEQ ID NO: 44)(SEQ ID NO: 759) 350 TTMP3 GAAAATATTGGTATTTTG (SEQ ID NO: 44)(SEQ ID NO: 760) 351 TIMP3 GGGATAAGCGAATTTTTT (SEQ ID NO: 44)(SEQ ID NO: 761) 352 TIMP3 GGGATAAGTGAATTTTTT (SEQ ID NO: 44)(SEQ ID NO: 762) 353 TIMP3 TTTTATTACGTATGTTTT (SEQ ID NO: 44)(SEQ ID NO: 763) 354 TIMP3 TTTTATTATGTATGTTTT (SEQ ID NO: 44)(SEQ ID NO: 764) 355 TP53 AAGTTGAACGTTTAGGTA (SEQ ID NO: 45)(SEQ ID NO: 765) 356 TP53 AAGTTGAATGTTTAGGTA (SEQ ID NO: 45)(SEQ ID NO: 766) 357 TP53 TTTTGAGTCGGTTTAAAG (SEQ ID NO: 45)(SEQ ID NO: 767) 358 TP53 TTTTGAGTTGGTTTAAAG (SEQ ID NO: 45)(SEQ ID NO: 768) 359 TP53 TATTTATTCGGTGTTGGG (SEQ ID NO: 45)(SEQ ID NO: 769) 360 TP53 TATTTATTTGGTGTTGGG (SEQ ID NO: 45)(SEQ ID NO: 770) 361 TP53 TTGGATTTCGAAATATTG (SEQ ID NO: 45)(SEQ ID NO: 771) 362 TP53 TTGGATTTTGAAATATTG (SEQ ID NO: 45)(SEQ ID NO: 772) 363 TP73 TGATTTAGCGTAGGTTTG (SEQ ID NO: 46)(SEQ ID NO: 773) 364 TP73 TGATTTAGTGTAGGTTTG (SEQ ID NO: 46)(SEQ ID NO: 774) 365 TP73 TTAGAGTTCGAGTTTATA (SEQ ID NO: 46)(SEQ ID NO: 775) 366 TP73 TTAGAGTTTGAGTTTATA (SEQ ID NO: 46)(SEQ ID NO: 776) 367 TP73 AAGTTACGGGTTTTATTG (SEQ ID NO: 46)(SEQ ID NO: 915) 368 TP73 AAGTTATGGGTTTTATTG (SEQ ID NO: 46)(SEQ ID NO: 916) 369 TP73 GGAAGTTTCGATGGTTTA (SEQ ID NO: 46)(SEQ ID NO: 777) 370 TP73 GGAAGTTTTGATGGTTTA (SEQ ID NO: 46)(SEQ ID NO: 778) 371 VHL TTTATAAGCGTGATGATT (SEQ ID NO: 47)(SEQ ID NO: 779) 372 VHL TTTATAAGTGTGATGATT (SEQ ID NO: 47)(SEQ ID NO: 780) 373 VHL GGTGTTTTCGTGTGAGAT (SEQ ID NO: 47)(SEQ ID NO: 781) 374 VHL GGTGTTTTTGTGTGAGAT (SEQ ID NO: 47)(SEQ ID NO: 782) 375 VHL TGTGAGATGCGTTATTTT (SEQ ID NO: 47)(SEQ ID NO: 783) 376 VHL TGTGAGATGTGTTATTTT (SEQ ID NO: 47)(SEQ ID NO: 784) 377 VHL TATATTGCGCGTTTGATA (SEQ ID NO: 47)(SEQ ID NO: 785) 378 VHL TATATTGTGTGTTTGATA (SEQ ID NO: 47)(SEQ ID NO: 786) 379 CDKN1C ATGAAGAACGGTTAAGGG (SEQ ID NO: 48)(SEQ ID NO: 787) 380 CDKN1C ATGAAGAATGGTTAAGGG (SEQ ID NO: 48)(SEQ ID NO: 788) 381 CDKN1C TTTTATTTCGAGTTAGGT (SEQ ID NO: 48)(SEQ ID NO: 789) 382 CDKN1C TTTTATTTCGAGTTAGGT (SEQ ID NO: 48)(SEQ ID NO: 790) 383 CDKN1C TTAAGTTACGGTTATTAG (SEQ ID NO: 48)(SEQ ID NO: 791) 384 CDKN1C TTAAGTTATGGTTATTAG (SEQ ID NO: 48)(SEQ ID NO: 792) 385 CDKN1C TTAGTGTTCGTTTGGAAT (SEQ ID NO: 48)(SEQ ID NO: 793) 386 CDKN1C TTAGTGTTTGTTTGGAAT (SEQ ID NO: 48)(SEQ ID NO: 794) 387 CAV1 TTGGTATCGTTGAAGAAT (SEQ ID NO: 49)(SEQ ID NO: 795) 388 CAV1 TTGGTATCGTTGAAGAAT (SEQ ID NO: 49)(SEQ ID NO: 796) 389 CAV1 TAGATTCGGAGGTAGGTA (SEQ ID NO: 49)(SEQ ID NO: 911) 390 CAV1 TAGATTTGGAGGTAGGTA (SEQ ID NO: 49)(SEQ ID NO: 912) 391 CAV1 TGGGGGTTCGAAAAAGTG (SEQ ID NO: 49)(SEQ ID NO: 797) 392 CAV1 TGGGGGTTTGAAAAAGTG (SEQ ID NO: 49)(SEQ ID NO: 798) 393 CAV1 GAAGTGTTCGTTTTTGTT (SEQ ID NO: 49)(SEQ ID NO: 799) 394 CAV1 GAAGTGTTTGTTTTTGTT (SEQ ID NO: 49)(SEQ ID NO: 800) 395 CDH13 GAAGTGGTCGTTAGTTTT (SEQ ID NO: 50)(SEQ ID NO: 801) 396 CDH13 GAAGTGGTTGTTAGTTTTT (SEQ ID NO: 50)(SEQ ID NO: 802) 397 CDH13 TTGTTTAGCGTGATTTGT (SEQ ID NO: 50)(SEQ ID NO: 803) 398 CDH13 TTGTTTAGTGTGATTTGT (SEQ ID NO: 50)(SEQ ID NO: 804) 399 CDH13 AAGGAATTCGTTTTGTAA (SEQ ID NO: 50)(SEQ ID NO: 903) 400 CDH13 AAGGAATTTGTTTTGTAA (SEQ ID NO: 50)(SEQ ID NO: 904) 401 CDH13 AATGTTTTCGTGATGTTG (SEQ ID NO: 50)(SEQ ID NO: 895) 402 CDH13 AATGTTTTTGTGATGTTG (SEQ ID NO: 50)(SEQ ID NO: 896) 403 DRG1 GAGTAGGACGGTGTTAAG (SEQ ID NO: 51)(SEQ ID NO: 805) 404 DRG1 GAGTAGGATGGTGTTAAG (SEQ ID NO: 51)(SEQ ID NO: 806) 405 DRG1 AAATTTAACGTTGGGTAG (SEQ ID NO: 51)(SEQ ID NO: 807) 406 DRG1 AAATTTAATGTTGGGTAG (SEQ ID NO: 51)(SEQ ID NO: 808) 407 DRG1 GATAATGACGGTGTTAGT (SEQ ID NO: 51)(SEQ ID NO: 809) 408 DRG1 GATAATGATGGTGTTAGT (SEQ ID NO: 51)(SEQ ID NO: 810) 409 DRG1 TGGTTGTACGTTAGGAGT (SEQ ID NO: 51)(SEQ ID NO: 811) 410 DRG1 TGGTTGTATGTTAGGAGT (SEQ ID NO: 51)(SEQ ID NO: 812) 411 PTGS2 TTTATTTTCGTGGGTAAA (SEQ ID NO: 52)(SEQ ID NO: 913) 412 PTGS2 TTTATTTTTGTGGGTAAA (SEQ ID NO: 52)(SEQ ID NO: 914) 413 PTGS2 AGTTATTTCGTTATATGG (SEQ ID NO: 52)(SEQ ID NO: 1007) 414 PTGS2 AGTTATTTTGTTATATGG (SEQ ID NO: 52)(SEQ ID NO: 1008) 415 PTGS2 ATTTAAGGCGATTAGTTT (SEQ ID NO: 52)(SEQ ID NO: 813) 416 PTGS2 ATTTAAGGTGATTAGTTT (SEQ ID NO: 52)(SEQ ID NO: 814) 417 PTGS2 ATATTTGGCGGAAATTTG (SEQ ID NO: 52)(SEQ ID NO: 1023) 418 PTGS2 ATATTTGGTGGAAATTTG (SEQ ID NO: 52)(SEQ ID NO: 1024) 419 THBS1 GGAGAGTTAGCGAGGGTT (SEQ ID NO: 53)(SEQ ID NO: 815) 420 THBS1 GGAGAGTTAGTGAGGGTT (SEQ ID NO: 53)(SEQ ID NO: 816) 421 THBS1 TATTTTAACGAATGGTTT (SEQ ID NO: 53)(SEQ ID NO: 817) 422 THBS1 TATTTTAATGAATGGTTT (SEQ ID NO: 53)(SEQ ID NO: 818) 423 THBS1 TTATAAAACGGGTTTAGT (SEQ ID NO: 53)(SEQ ID NO: 819) 424 THBS1 TTATAAAATGGGTTTAGT (SEQ ID NO: 53)(SEQ ID NO: 820) 425 THBS1 AGGTATTTCGGGAGATTA (SEQ ID NO: 53)(SEQ ID NO: 821) 426 THBS1 AGGTATTTTGGGAGATTA (SEQ ID NO: 53)(SEQ ID NO: 822) 427 TPEF ATTTGTTTCGATTAATTT (= TMEFF2 = HPP1)(SEQ ID NO: 979) (SEQ ID NO: 54) 428 TPEF ATTTGTTTTGATTAATTT (= TMEFF2 =HPP1) (SEQ ID NO: 980) (SEQ ID NO: 54) 429 TPEF ATAGGTTACGGGTTGGAG (=TMEFF2; = HPP1) (SEQ ID NO: 917) (SEQ ID NO: 54) 430 TPEFATAGGTTATGGGTTGGAG (= TMEFF2; = HPP1) (SEQ ID NO: 918) (SEQ ID NO: 54)431 TPEF AATTTGCGAACGTTTGGG (= TMEFF2; = HPP1) (SEQ ID NO: 899)(SEQ ID NO: 54) 432 TPEF AATTTGTGAATGTTTGGG (= TMEFF2; = HPP1)(SEQ ID NO: 900) (SEQ ID NO: 54) 433 DNMT1 AGTGGGTTCGTTTAAGTT(SEQ ID NO: 55) (SEQ ID NO: 823) 434 DNMT1 AGTGGGTTTGTTTAAGTT(SEQ ID NO: 55) (SEQ ID NO: 824) 435 DNMT1 TTTTTTACGCGGAGTAGT(SEQ ID NO: 55) (SEQ ID NO: 825) 436 DNMT1 TTTTTTATGTGGAGTAGT(SEQ ID NO: 55) (SEQ ID NO: 826) 437 DNMT1 GAGAGAGGCGATATTTTG(SEQ ID NO: 55) (SEQ ID NO: 827) 438 DNMT1 GAGAGAGGTGATATTTTG(SEQ ID NO: 55) (SEQ ID NO: 828) 439 DNMT1 GTATTAAACGGAGAGAGG(SEQ ID NO: 55) (SEQ ID NO: 829) 440 DNMT1 GTATTAAATGGAGAGAGG(SEQ ID NO: 55) (SEQ ID NO: 830) 441 CEA AAGTGTTCGCGGTTGTTT(SEQ ID NO: 56) (SEQ ID NO: 1003) 442 CEA AAGTGTTTGTGGTTGTTT(SEQ ID NO: 56) (SEQ ID NO: 1004) 443 CEA TTTTGAGTCGTAGTTTAG(SEQ ID NO: 56) (SEQ ID NO: 831) 444 CEA TTTGAGTTGTAGTTTAG(SEQ ID NO: 56) (SEQ ID NO: 832) 445 CEA AA TAGATACGGAGAGGGA(SEQ ID NO: 56) (SEQ ID NO: 833) 446 CEA AATAGATATGGAGAGGGA(SEQ ID NO: 56) (SEQ ID NO: 834) 447 MB AGAAGGTGCGTGAGAGGT(SEQ ID NO: 57) (SEQ ID NO: 835) 448 MB AGAAGGTGTGTGAGAGGT(SEQ ID NO: 57) (SEQ ID NO: 836) 449 MB GGGTTAGTCGGGGTATTT(SEQ ID NO: 57) (SEQ ID NO: 837) 450 MB GGGTTAGTTGGGGTATTT(SEQ ID NO: 57) (SEQ ID NO: 838) 451 MB GGGGATAGCGAGTTATTG(SEQ ID NO: 57) (SEQ ID NO: 839) 452 MB GGGGATAGTGAGTTATTG(SEQ ID NO: 57) (SEQ ID NO: 840) 453 MB TTAGATTGCGTTATGGGG(SEQ ID NO: 57) (SEQ ID NO: 841) 454 MB TTAGATTGTGTTATGGGG(SEQ ID NO: 57) (SEQ ID NO: 842) 455 PCNA TAAAGAGGCGGGGAGATT(SEQ ID NO: 58) (SEQ ID NO: 1013) 456 PCNA TAAAGAGGTGGGGAGATT(SEQ ID NO: 58) (SEQ ID NO: 1014) 457 PCNA TATGGATACGATTGGTTT(SEQ ID NO: 58) (SEQ ID NO: 843) 458 PCNA TATGGATATGATTGGTTT(SEQ ID NO: 58) (SEQ ID NO: 844) 459 PCNA GTATTAAACGGTTGTAGG(SEQ ID NO: 58) (SEQ ID NO: 845) 460 PCNA GTATTAAATGGTTGTAGG(SEQ ID NO: 58) (SEQ ID NO: 846) 461 PCNA TTTGAAGTCGAAATTAGT(SEQ ID NO: 58) (SEQ ID NO: 847) 462 PCNA TTTGAAGTTGAAATTAGT(SEQ ID NO: 58) (SEQ ID NO: 848) 463 CDC2 TGGAATTTCGATGTAAAT(SEQ ID NO: 59) (SEQ ID NO: 849) 464 CDC2 TGGAATTTTGATGTAAAT(SEQ ID NO: 59) (SEQ ID NO: 850) 465 CDC2 TAGTAGGACGATATTTTT(SEQ ID NO: 59) (SEQ ID NO: 851) 466 CDC2 TAGTAGGATGATATTTTT(SEQ ID NO: 59) (SEQ ID NO: 852) 467 CDC2 TAGTTATTCGGGAAGGTT(SEQ ID NO: 59) (SEQ ID NO: 853) 468 CDC2 TAGTTATTTGGGAAGGTT(SEQ ID NO: 59) (SEQ ID NO: 854) 469 CDC2 AAATTGTTCGTATTTGGT(SEQ ID NO: 59) (SEQ ID NO: 855) 470 CDC2 AAATTGTTTGTATTTGGT(SEQ ID NO: 59) (SEQ ID NO: 856) 471 ESR1 AGATATATCGGAGTTTGG(SEQ ID NO: 60) (SEQ ID NO: 857) 472 ESR1 AGATATATTGGAGTTTGG(SEQ ID NO: 60) (SEQ ID NO: 858) 473 ESR1 GTTTGGTACGGGGTATAT(SEQ ID NO: 60) (SEQ ID NO: 859) 474 ESR1 GTTTGGTATGGGGTATAT(SEQ ID NO: 60) (SEQ ID NO: 860) 475 ESR1 TTTTAAATCGAGTTGTGT(SEQ ID NO: 60) (SEQ ID NO: 861) 476 ESR1 TTTTAAATTGAGTTGTGT(SEQ ID NO: 60) (SEQ ID NO: 862) 477 ESR1 TATGAGTTCGGGAGATTA(SEQ ID NO: 60) (SEQ ID NO: 863) 478 ESR1 TATGAGTTTGGGAGATTA(SEQ ID NO: 60) (SEQ ID NO: 864) 479 ESR1 TGGAGGTTCGGGAGTTTA(SEQ ID NO: 60) (SEQ ID NO: 969) 480 ESR1 TGGAGGTTTGGGAGTTTA(SEQ ID NO: 60) (SEQ ID NO: 970) 481 CASP8 GAATGAGTCGAGGAAGGT(SEQ ID NO: 61) (SEQ ID NO: 865) 482 CASP8 GAATGAGTTGAGGAAGGT(SEQ ID NO: 61) (SEQ ID NO: 866) 483 CASP8 TATTGAGACGTTAAGTAA(SEQ ID NO: 61) (SEQ ID NO: 867) 484 CASP8 TATTGAGATGTTAAGTAA(SEQ ID NO: 61) (SEQ ID NO: 868) 485 CASP8 TAAGGTTACGTAGTTAGT(SEQ ID NO: 61) (SEQ ID NO: 869) 486 CASP8 TAAGGTTATGTAGTTAGT(SEQ ID NO: 61) (SEQ ID NO: 870) 487 CASP8 GTTAATAGCGGGGATTTT(SEQ ID NO: 61) (SEQ ID NO: 871) 488 CASP8 GTTAATAGTGGGGATTTT(SEQ ID NO: 61) (SEQ ID NO: 872) 489 RASSF1 GTAGTTTTCGAGAATGTT(SEQ ID NO: 62) (SEQ ID NO: 873) 490 RASSF1 GTAGTTTTTGAGAATGTT(SEQ ID NO: 62) (SEQ ID NO: 874) 491 RASSF1 TAATTAGAACGTTTTTTG(SEQ ID NO: 62) (SEQ ID NO: 875) 492 RASSF1 TAATTAGAATGTTTTTTG(SEQ ID NO: 62) (SEQ ID NO: 876) 493 RASSF1 TAGTTTTCGCGTAGAATT(SEQ ID NO: 62) (SEQ ID NO: 877) 494 RASSF1 TAGTTTTTGTGTAGAATT(SEQ ID NO: 62) (SEQ ID NO: 878) 495 RASSF1 TTTGTAGCGGGTGGAGTA(SEQ ID NO: 62) (SEQ ID NO: 995) 496 RASSF1 TTTGTAGTGGGTGGAGTA(SEQ ID NO: 62) (SEQ ID NO: 996) 497 MSH4 TTGTTTCGGCGGTTTTTT(SEQ ID NO: 63) (SEQ ID NO: 879) 498 MSH4 TTGTTTTGGTGGTTTTTT(SEQ ID NO: 63) (SEQ ID NO: 880) 499 MSH4 TTTTGGTACGTTAGGAGT(SEQ ID NO: 63) (SEQ ID NO: 881) 500 MSH4 TTTTGGTATGTTAGGAGT(SEQ ID NO: 63) (SEQ ID NO: 882) 501 MSH4 TAAATTTTCGGTTAGTTT(SEQ ID NO: 63) (SEQ ID NO: 883) 502 MSH4 TAAATTTTTGGTTAGTTT(SEQ ID NO: 63) (SEQ ID NO: 884) 503 MSH4 TTAGAGGTCGGTAGTTTA(SEQ ID NO: 63) (SEQ ID NO: 885) 504 MSH4 TTAGAGGTTGGTAGTTTA(SEQ ID NO: 63) (SEQ ID NO: 886) 505 MSH5 ATGTTTATCGTTTTGAGT(SEQ ID NO: 64) (SEQ ID NO: 887) 506 MSH5 ATGTTTATTGTTTTGAGT(SEQ ID NO: 64) (SEQ ID NO: 888) 507 MSH5 ATAGTTGTCGAATGTATG(SEQ ID NO: 64) (SEQ ID NO: 889) 508 MSH5 ATAGTTGTTGAATGTATG(SEQ ID NO: 64) (SEQ ID NO: 890) 509 MSH5 TAGAAGTGCGAAGGGGTA(SEQ ID NO: 64) (SEQ ID NO: 891) 510 MSH5 TAGAAGTGTGAAGGGGTA(SEQ ID NO: 64) (SEQ ID NO: 892) 511 MSH5 ATGTAATTCGAATGTTTT(SEQ ID NO: 64) (SEQ ID NO: 893) 512 MSH5 ATGTAATTTGAATGTTTT(SEQ ID NO: 64) (SEQ ID NO: 894)

TABLE 3 Oligonucleotides used in differentiation betweencolon adenomas or carcinoma tissue and healthy colon tissue. No: GeneOligo: 1 CDH13 AATGTTTTCGTGATGTTG (SEQ ID NO: 50) (SEQ ID NO: 895) 2CDH13 AATGTTTTTGTGATGTTG (SEQ ID NO: 50) (SEQ ID NO: 896) 3 CD44TTGTTTAGCGGATTTTAG (SEQ ID NO: 20) (SEQ ID NO: 897) 4 CD44TTGTTTAGTGGATTTTAG (SEQ ID NO: 20) (SEQ ID NO: 898) 5 TPEFAATTTGCGAACGTTTGGG (= TMEFF2; = HPP1) (SEQ ID NO: 899) (SEQ ID NO: 54) 6TPEF AATTTGTGAATGTTTGGG (= TMEFF2; = HPP1) (SEQ ID NO: 900)(SEQ ID NO: 54) 7 CSPG2 GGGTAACGTCGAATTTAG (SEQ ID NO: 21)(SEQ ID NO: 901) 8 CSPG2 GGGTAATGTTGAATTTAG (SEQ ID NO: 21)(SEQ ID NO: 902) 9 CDH13 AAGGAATTCGTTTTGTAA (SEQ ID NO: 50)(SEQ ID NO: 903) 10 CDH13 AAGGAATTTGTTTTGTAA (SEQ ID NO: 50)(SEQ ID NO: 904) 11 GSTP1 GGAGTTCGCGGGATTTTT (SEQ ID NO: 25)(SEQ ID NO: 905) 12 GSTP1 GGAGTTTGTGGGATTTTT (SEQ ID NO: 25)(SEQ ID NO: 906) 13 TGFBR2 AAAGTTTTCGGAGGGGTT (SEQ ID NO: 43)(SEQ ID NO: 907) 14 TGFBR2 AAAGTTTTTGGAGGGGTT (SEQ ID NO: 43)(SEQ ID NO: 908) 15 N33 TGTTATTTCGGAGGGTTT (SEQ ID NO: 36)(SEQ ID NO: 909) 16 N33 TGTTATTTTGGAGGGTTT (SEQ ID NO: 36)(SEQ ID NO: 910) 17 CAV1 TAGATTCGGAGGTAGGTA (SEQ ID NO: 49)(SEQ ID NO: 911) 18 CAV1 TAGATTTGGAGGTAGGTA (SEQ ID NO: 49)(SEQ ID NO: 912) 19 PTGS2 TTTATTTTCGTGGGTAAA (SEQ ID NO: 52)(SEQ ID NO: 913) 20 PTGS2 TTTATTTTTGTGGGTAAA (SEQ ID NO: 52)(SEQ ID NO: 914) 21 TP73 AAGTTACGGGTTTTATTG (SEQ ID NO: 46)(SEQ ID NO: 915) 22 TP73 AAGTTATGGGTTTTATTG (SEQ ID NO: 46)(SEQ ID NO: 916) 23 TPEF ATAGGTTACGGGTTGGAG (= TMEFF2; = HPP1)(SEQ ID NO: 917) (SEQ ID NO: 54) 24 TPEF ATAGGTTATGGGTTGGAG (= TMEFF2; =HPP1) (SEQ ID NO: 918) (SEQ ID NO: 54) 25 CD44 GTGGGGTTCGGAGGTATA(SEQ ID NO: 20) (SEQ ID NO: 919) 26 CD44 GTGGGGTTTGGAGGTATA(SEQ ID NO: 20) (SEQ ID NO: 920) 27 EYA4 AAGTAAGTCGTTGTTGTT(SEQ ID NO: 24) (SEQ ID NO: 921) 28 EYA4 AAGTAAGTTGTTGTTGTT(SEQ ID NO: 24) (SEQ ID NO: 922) 29 EYA4 AGTGTATGCGTAGAAGGT(SEQ ID NO: 24) (SEQ ID NO: 923) 30 EYA4 AGTGTATGTGTAGAAGGT(SEQ ID NO: 24) (SEQ ID NO: 924) 31 GTBP/MSH6 TTTGTTGGCGGGAAATTT(SEQ ID NO: 26) (SEQ ID NO: 925) 32 GTBP/MSH6 TTTGTTGGTGGGAAATTT(SEQ ID NO: 26) (SEQ ID NO: 926) 33 EGR4 GGAGTTTTCGGTATATAT(SEQ ID NO: 4) (SEQ ID NO: 927) 34 EGR4 GGAGTTTTTGGTATATAT(SEQ ID NO: 4) (SEQ ID NO: 928) 35 CDH1 TAGTGGCGTCGGAATTGT(SEQ ID NO: 15) (SEQ ID NO: 929) 36 CDH1 TAGTGGTGTTGGAATTGT(SEQ ID NO: 15) (SEQ ID NO: 930) 37 EGFR ATTTGGTTCGATTTGGAT(SEQ ID NO: 23) (SEQ ID NO: 931) 38 EGFR ATTTGGTTTGATTTGGAT(SEQ ID NO: 23) (SEQ ID NO: 932) 39 LKB1 AGGGAGGTCGTTGGTATT(SEQ ID NO: 30) (SEQ ID NO: 933) 40 LKB1 AGGGAGGTTGTTGGTATT(SEQ ID NO: 30) (SEQ ID NO: 934) 41 DAPK1 TTGTTTTTCGGAAATTTG(SEQ ID NO: 22) (SEQ ID NO: 935) 42 DAPK1 TTGTTTTTTGGAAATTTG(SEQ ID NO: 22) (SEQ ID NO: 936) 43 IGF2 GATTAGGGCGGGAAATAT(SEQ ID NO: 29) (SEQ ID NO: 937) 44 IGF2 GATTAGGGTGGGAAATAT(SEQ ID NO: 29) (SEQ ID NO: 938) 45 HLA-F TATTTGGGCGGGTGAGTG(SEQ ID NO: 10) (SEQ ID NO: 939) 46 HLA-F TATTTGGGTGGGTGAGTG(SEQ ID NO: 10) (SEQ ID NO: 940) 47 IGF2 TTGTATGGTCGAGTTTAT(SEQ ID NO: 29) (SEQ ID NO: 941) 48 IGF2 TTGTATGGTTGAGTTTAT(SEQ ID NO: 29) (SEQ ID NO: 942) 49 N33 GTTTAGTTAGCGGGTTTT(SEQ ID NO: 36) (SEQ ID NO: 943) 50 N33 GTTTAGTTAGTGGGTTTT(SEQ ID NO: 36) (SEQ ID NO: 944) 51 CSPG2 AAAAATTCGCGAGTTTAG(SEQ ID NO: 21) (SEQ ID NO: 945) 52 CSPG2 AAAAATTTGTGAGTTTAG(SEQ ID NO: 21) (SEQ ID NO: 946) 53 PTEN TGATGTGGCGGGATTTTT(SEQ ID NO: 39) (SEQ ID NO: 947) 54 PTEN TGATGTGGTGGGATTTTT(SEQ ID NO: 39) (SEQ ID NO: 948) 55 MLH1 TTAGGTAGCGGGTAGTAG(SEQ ID NO: 32) (SEQ ID NO: 949) 56 MLH1 TTAGGTAGTGGGTAGTAG(SEQ ID NO: 32) (SEQ ID NO: 950) 57 GTBP/MSH6 GAGGAATTCGGGTTTTAG(SEQ ID NO: 26) (SEQ ID NO: 951) 58 GTBP/MSH6 GAGGAATTTGGGTTTTAG(SEQ ID NO: 26) (SEQ ID NO: 952) 59 CALCA ATTAGGTTCGTGTTTTAG(SEQ ID NO: 14) (SEQ ID NO: 953) 60 CALCA ATTAGGTTTGTGTTTTAG(SEQ ID NO: 14) (SEQ ID NO: 954) 61 DAPK1 GAAGGGAGCGTATTTTAT(SEQ ID NO: 22) (SEQ ID NO: 955) 62 DAPK1 GAAGGGAGCGTATTTTAT(SEQ ID NO: 22) (SEQ ID NO: 956) 63 PTEN AGAGTTATCGTTTTGTTT(SEQ ID NO: 39) (SEQ ID NO: 957) 64 PTEN AGAGTTATTGTTTTGTTT(SEQ ID NO: 39) (SEQ ID NO: 958) 65 WT1 TGTTATATCGGTTAGTTG(SEQ ID NO: 9) (SEQ ID NO: 959) 66 WT1 TGTTATATTGGTTAGTTG (SEQ ID NO: 9)(SEQ ID NO: 960) 67 EGFR TTTGTATTCGGAGTTGGG (SEQ ID NO: 23)(SEQ ID NO: 961) 68 EGFR TTTGTATTTGGAGTTGGG (SEQ ID NO: 23)(SEQ ID NO: 962) 69 CSPG2 AAGATTTTCGGTTAGTTT (SEQ ID NO: 21)(SEQ ID NO: 963) 70 CSPG2 AAGATTTTTGGTTAGTTT (SEQ ID NO: 21)(SEQ ID NO: 964) 71 LKB1 TTTAGGTTCGTAAGTTTA (SEQ ID NO: 30)(SEQ ID NO: 965) 72 LKB1 TTTAGGTTTGTAAGTTTA (SEQ ID NO: 30)(SEQ ID NO: 966) 73 WT1 TATATTGGCGAAGGTTAA (SEQ ID NO: 9)(SEQ ID NO: 967) 74 WT1 TATATTGGTGAAGGTTAA (SEQ ID NO: 9)(SEQ ID NO: 968) 75 ESR1 TGGAGGTTCGGGAGTTTA (SEQ ID NO: 60)(SEQ ID NO: 969) 76 ESR1 TGGAGGTTTGGGAGTTTA (SEQ ID NO: 60)(SEQ ID NO: 970) 77 APC TTTAATCGTATAGTTTGT (SEQ ID NO: 12)(SEQ ID NO: 971) 78 APC TTTAATTGTATAGTTTGT (SEQ ID NO: 12)(SEQ ID NO: 972) 79 IGF2 AGTTTGAACGATGTAAGA (SEQ ID NO: 29)(SEQ ID NO: 973) 80 IGF2 AGTTTGAATGATGTAAGA (SEQ ID NO: 29)(SEQ ID NO: 974) 81 MYOD1 AATTAGGTCGGATAGGAG (SEQ ID NO: 8)(SEQ ID NO: 975) 82 MYOD1 AATTAGGTTGGATAGGAG (SEQ ID NO: 8)(SEQ ID NO: 976) 83 N33 TTGGTTCGGGAAAGGTAA (SEQ ID NO: 36)(SEQ ID NO: 977) 84 N33 TTGGTTTGGGAAAGGTAA (SEQ ID NO: 36)(SEQ ID NO: 978) 85 TPEF ATTTGTTTCGATTAATTT (= TMEFF2; = HPP1)(SEQ ID NO: 979) (SEQ ID NO: 54) 86 TPEF ATTTGTTTTGATTAATTT (= TMEFF2; =HPP1) (SEQ ID NO: 980) (SEQ ID NO: 54) 87 CDKN2a AATAGTTACGGTCGGAGG(SEQ ID NO: 18) (SEQ ID NO: 981) 88 CDKN2a AATAGTTATGGTTGGAGG(SEQ ID NO: 18) (SEQ ID NO: 982) 89 CDH1 AGGGTTATCGCGTTTATG(SEQ ID NO: 15) (SEQ ID NO: 983) 90 CDH1 AGGGTTATTGTGTTTATG(SEQ ID NO: 15) (SEQ ID NO: 984) 91 APC TATTTTGGCGGGTTGTAT(SEQ ID NO: 12) (SEQ ID NO: 985) 92 APC TATTTTGGTGGGTTGTAT(SEQ ID NO: 12) (SEQ ID NO: 986)

TABLE 4 Oligonucleotides used in differentiation betweencolon carcinoma tissue and healthy colon tissue. No: Gene Oligo: 1 CDH13AATGTTTTCGTGATGTTG (SEQ ID NO: 50) (SEQ ID NO: 895) 2 CDH13AATGTTTTTGTGATGTTG (SEQ ID NO: 50) (SEQ ID NO: 896) 3 TPEFAATTTGCGAACGTTTGGG (= TMEFF2; = HPP1) (SEQ ID NO: 899) (SEQ ID NO: 54) 4TPEF AATTTGTGAATGTTTGGG (= TMEFF2; = HPP1) (SEQ ID NO: 900)(SEQ ID NO: 54) 5 CDH13 AAGGAATTCGTTTTGTAA (SEQ ID NO: 50)(SEQ ID NO: 903) 6 CDH13 AAGGAATTTGTTTTGTAA (SEQ ID NO: 50)(SEQ ID NO: 904) 7 CSPG2 GGGTAACGTCGAATTTAG (SEQ ID NO: 21)(SEQ ID NO: 901) 8 CSPG2 GGGTAATGTTGAATTTAG (SEQ ID NO: 21)(SEQ ID NO: 902) 9 CD44 TTGTTTAGCGGATTTTAG (SEQ ID NO: 20)(SEQ ID NO: 897) 10 CD44 TTGTTTAGTGGATTTTAG (SEQ ID NO: 20)(SEQ ID NO: 898) 11 EYA4 AGTGTATGCGTAGAAGGT (SEQ ID NO: 24)(SEQ ID NO: 923) 12 EYA4 AGTGTATGTGTAGAAGGT (SEQ ID NO: 24)(SEQ ID NO: 924) 13 APC TTTAATCGTATAGTTTGT (SEQ ID NO: 12)(SEQ ID NO: 971) 14 APC TTTAATTGTATAGTTTGT (SEQ ID NO: 12)(SEQ ID NO: 972) 15 PTGS2 TTTATTTTCGTGGGTAAA (SEQ ID NO: 52)(SEQ ID NO: 913) 16 PTGS2 TTTATTTTTGTGGGTAAA (SEQ ID NO: 52)(SEQ ID NO: 914) 17 EYA4 AAGTAAGTCGTTGTTGTT (SEQ ID NO: 24)(SEQ ID NO: 921) 18 EYA4 AAGTAAGTTGTTGTTGTT (SEQ ID NO: 24)(SEQ ID NO: 922) 19 PTEN ATTTTGCGTTCGTATTTA (SEQ ID NO: 39)(SEQ ID NO: 987) 20 PTEN ATTTTGTGTTTGTATTTA (SEQ ID NO: 39)(SEQ ID NO: 988) 21 GSTP1 GGAGTTCGCGGGATTTTT (SEQ ID NO: 25)(SEQ ID NO: 905) 22 GSTP1 GGAGTTTGTGGGATTTTT (SEQ ID NO: 25)(SEQ ID NO: 906) 23 CAV1 TAGATTCGGAGGTAGGTA (SEQ ID NO: 49)(SEQ ID NO: 911) 24 CAV1 TAGATTTGGAGGTAGGTA (SEQ ID NO: 49)(SEQ ID NO: 912) 25 EGFR ATTTGGTTCGATTTGGAT (SEQ ID NO: 23)(SEQ ID NO: 931) 26 EGFR ATTTGGTTTGATTTGGAT (SEQ ID NO: 23)(SEQ ID NO: 932) 27 N33 TGTTATTTCGGAGGGTTT (SEQ ID NO: 36)(SEQ ID NO: 909) 28 N33 TGTTATTTTGGAGGGTTT (SEQ ID NO: 36)(SEQ ID NO: 910) 29 IGF2 TTGTATGGTCGAGTTTAT (SEQ ID NO: 29)(SEQ ID NO: 941) 30 IGF2 TTGTATGGTTGAGTTTAT (SEQ ID NO: 29)(SEQ ID NO: 942) 31 HLA-F AGTTGTTTCGTAGATATT (SEQ ID NO: 10)(SEQ ID NO: 989) 32 HLA-F AGTTGTTTTGTAGATATT (SEQ ID NO: 10)(SEQ ID NO: 990) 33 TPEF ATAGGTTACGGGTTGGAG (= TMEFF2; = HPP1)(SEQ ID NO: 917) (SEQ ID NO: 54) 34 TPEF ATAGGTTATGGGTTGGAG (= TMEFF2; =HPP1) (SEQ ID NO: 918) (SEQ ID NO: 54) 35 TP73 AAGTTACGGGTTTTATTG(SEQ ID NO: 46) (SEQ ID NO: 915) 36 TP73 AAGTTATGGGTTTTATTG(SEQ ID NO: 46) (SEQ ID NO: 916)

TABLE 5 Oligonucleotides used in differentiation betweencolon adenoma tissue and healthy colon tissue. No: Gene Oligo: 1 CD44TTGTTTAGCGGATTTTAG (SEQ ID NO: 20) (SEQ ID NO: 897) 2 CD44TTGTTTAGTGGATTTTAG (SEQ ID NO: 20) (SEQ ID NO: 898) 3 HLA-FTATTTGGGCGGGTGAGTG (SEQ ID NO: 10) (SEQ ID NO: 939) 4 HLA-FTATTTGGGTGGGTGAGTG (SEQ ID NO: 10) (SEQ ID NO: 940) 5 TGFBR2AAAGTTTTCGGAGGGGTT (SEQ ID NO: 43) (SEQ ID NO: 907) 6 TGFBR2AAAGTTTTTGGAGGGGTT (SEQ ID NO: 43) (SEQ ID NO: 908) 7 GTBP/MSH6GAGGAATTCGGGTTTTAG (SEQ ID NO: 26) (SEQ ID NO: 951) 8 GTBP/MSH6GAGGAATTTGGGTTTTAG (SEQ ID NO: 26) (SEQ ID NO: 952) 9 GTBP/MSH6TTTGTTGGCGGGAAATTT (SEQ ID NO: 26) (SEQ ID NO: 925) 10 GTBP/MSH6TTTGTTGGTGGGAAATTT (SEQ ID NO: 26) (SEQ ID NO: 926) 11 LKB1AGGGAGGTCGTTGGTATT (SEQ ID NO: 30) (SEQ ID NO: 933) 12 LKB1AGGGAGGTTGTTGGTATT (SEQ ID NO: 30) (SEQ ID NO: 934) 13 CD44GTGGGGTTCGGAGGTATA (SEQ ID NO: 20) (SEQ ID NO: 919) 14 CD44GTGGGGTTTGGAGGTATA (SEQ ID NO: 20) (SEQ ID NO: 920) 15 N33GTTTAGTTAGCGGGTTTT (SEQ ID NO: 36) (SEQ ID NO: 943) 16 N33GTTTAGTTAGTGGGTTTT (SEQ ID NO: 36) (SEQ ID NO: 944) 17 CDH13AATGTTTTCGTGATGTTG (SEQ ID NO: 50) (SEQ ID NO: 895) 18 CDH13AATGTTTTTGTGATGTTG (SEQ ID NO: 50) (SEQ ID NO: 896) 19 TP73AAGTTACGGGTTTTATTG (SEQ ID NO: 46) (SEQ ID NO: 915) 20 TP73AAGTTATGGGTTTTATTG (SEQ ID NO: 46) (SEQ ID NO: 916) 21 PTENTGATGTGGCGGGATTTTT (SEQ ID NO: 39) (SEQ ID NO: 947) 22 PTENTGATGTGGTGGGATTTTT (SEQ ID NO: 39) (SEQ ID NO: 948) 23 N33TGTTATTTCGGAGGGTTT (SEQ ID NO: 36) (SEQ ID NO: 909) 24 N33TGTTATTTTGGAGGGTTT (SEQ ID NO: 36) (SEQ ID NO: 910) 25 TPEFAATTTGCGAACGTTTGGG (= TMEFF2; = HPP1) (SEQ ID NO: 899) (SEQ ID NO: 54)26 TPEF AATTTGTGAATGTTTGGG (= TMEFF2; = HPP1) (SEQ ID NO: 900)(SEQ ID NO: 54) 27 GSTP1 GGAGTTCGCGGGATTTTT (SEQ ID NO: 25)(SEQ ID NO: 905) 28 GSTP1 GGAGTTTGTGGGATTTTT (SEQ ID NO: 25)(SEQ ID NO: 906) 29 EGFR TTTGTATTCGGAGTTGGG (SEQ ID NO: 23)(SEQ ID NO: 961) 30 EGFR TTTGTATTTGGAGTTGGG (SEQ ID NO: 23)(SEQ ID NO: 962) 31 RARB TAGTAGTTCGGGTAGGGT (SEQ ID NO: 40)(SEQ ID NO: 991) 32 RARB TAGTAGTTTGGGTAGGGT (SEQ ID NO: 40)(SEQ ID NO: 992) 33 N33 Al 1TAGTTCGGGGGAGGA (SEQ ID NO: 36)(SEQ ID NO: 993) 34 N33 ATTTAGTTTGGGGGAGGA (SEQ ID NO: 36)(SEQ ID NO: 994) 35 CAV1 TAGATTCGGAGGTAGGTA (SEQ ID NO: 49)(SEQ ID NO: 911) 36 CAV1 TAGATTTGGAGGTAGGTA (SEQ ID NO: 49)(SEQ ID NO: 912) 37 TPEF ATAGGTTACGGGTTGGAG (= TMEFF2; = HPP1)(SEQ ID NO: 917) (SEQ ID NO: 54) 38 TPEF ATAGGTTATGGGTTGGAG (= TMEFF2; =HPP1) (SEQ ID NO: 918) (SEQ ID NO: 54) 39 CDKN2a AATAGTTACGGTCGGAGG(SEQ ID NO: 18) (SEQ ID NO: 981) 40 CDKN2a AATAGTTATGGTTGGAGG(SEQ ID NO: 18) (SEQ ID NO: 982) 41 N33 TTGGTTCGGGAAAGGTAA(SEQ ID NO: 36) (SEQ ID NO: 977) 42 N33 TTGGTTTGGGAAAGGTAA(SEQ ID NO: 36) (SEQ ID NO: 978) 43 MLH1 TTAGGTAGCGGGTAGTAG(SEQ ID NO: 32) (SEQ ID NO: 949) 44 MLH1 TTAGGTAGTGGGTAGTAG(SEQ ID NO: 32) (SEQ ID NO: 950) 45 APC TATTTTGGCGGGTTGTAT(SEQ ID NO: 12) (SEQ ID NO: 985) 46 APC TATTTTGGTGGGTTGTAT(SEQ ID NO: 12) (SEQ ID NO: 986) 47 CSPG2 GGGTAACGTCGAATTTAG(SEQ ID NO: 21) (SEQ ID NO: 901) 48 CSPG2 GGGTAATGTTGAATTTAG(SEQ ID NO: 21) (SEQ ID NO: 902) 49 CDH1 TAGTGGCGTCGGAATTGT(SEQ ID NO: 15) (SEQ ID NO: 929) 50 CDH1 TAGTGGTGTTGGAATTGT(SEQ ID NO: 15) (SEQ ID NO: 930) 51 PTGS2 TTTATTTTCGTGGGTAAA(SEQ ID NO: 52) (SEQ ID NO: 913) 52 PTGS2 TTTATTTTTGTGGGTAAA(SEQ ID NO: 52) (SEQ ID NO: 914) 53 RASSF1 TTTGTAGCGGGTGGAGTA(SEQ ID NO: 62) (SEQ ID NO: 995) 54 RASSF1 TTTGTAGTGGGTGGAGTA(SEQ ID NO: 62) (SEQ ID NO: 996) 55 WT1 TATATTGGCGAAGGTTAA(SEQ ID NO: 9) (SEQ ID NO: 967) 56 WT1 TATATTGGTGAAGGTTAA (SEQ ID NO: 9)(SEQ ID NO: 968) 57 CDKN2a GGAGTTTTCGGTTGATTG (SEQ ID NO: 18)(SEQ ID NO: 997) 58 CDKN2a GGAGTTTTTGGTTGATTG (SEQ ID NO: 18)(SEQ ID NO: 998) 59 ESR1 TGGAGGTTCGGGAGTTTA (SEQ ID NO: 60)(SEQ ID NO: 969) 60 ESR1 TGGAGGTTTGGGAGTTTA (SEQ ID NO: 60)(SEQ ID NO: 970) 61 IGF2 GATTAGGGCGGGAAATAT (SEQ ID NO: 29)(SEQ ID NO: 937) 62 IGF2 GATTAGGGTGGGAAATAT (SEQ ID NO: 29)(SEQ ID NO: 938) 63 MYOD1 AATTAGGTCGGATAGGAG (SEQ ID NO: 8)(SEQ ID NO: 975) 64 MYOD1 AATTAGGTTGGATAGGAG (SEQ ID NO: 8)(SEQ ID NO: 976) 65 CDH13 AAGGAATTCGTTTTGTAA (SEQ ID NO: 50)(SEQ ID NO: 903) 66 CDH13 AAGGAATTTGTTTTGTAA (SEQ ID NO: 50)(SEQ ID NO: 904) 67 EGR4 GGAGTTTTCGGTATATAT (SEQ ID NO: 4)(SEQ ID NO: 927) 68 EGR4 GGAGTTTTTGGTATATAT (SEQ ID NO: 4)(SEQ ID NO: 928) 69 S100A2 TATGTATACGAGTATTGG (SEQ ID NO: 42)(SEQ ID NO: 999) 70 S100A2 TATGTATATGAGTATTGG (SEQ ID NO: 42)(SEQ ID NO: 1000) 71 DAPK1 TTGTTTTTCGGAAATTTG (SEQ ID NO: 22)(SEQ ID NO: 935) 72 DAPK1 TTGTTTTTTGGAAATTTG (SEQ ID NO: 22)(SEQ ID NO: 936) 73 MGMT AGTAGGATCGGGATTTTT (SEQ ID NO: 31)(SEQ ID NO: 1001) 74 MGMT AGTAGGATTGGGATTTTT (SEQ ID NO: 31)(SEQ ID NO: 1002) 75 EYA4 AAGTAAGTCGTTGTTGTT (SEQ ID NO: 24)(SEQ ID NO: 921) 76 EYA4 AAGTAAGTTGTTGTTGTT (SEQ ID NO: 24)(SEQ ID NO: 922) 77 CEA AAGTGTTCGCGGTTGTTT (SEQ ID NO: 56)(SEQ ID NO: 1003) 78 CEA AAGTGTTTGTGGTTGTTT (SEQ ID NO: 56)(SEQ ID NO: 1004) 79 WT1 TGTTATATCGGTTAGTTG (SEQ ID NO: 9)(SEQ ID NO: 959) 80 WT1 TGTTATATTGGTTAGTTG (SEQ ID NO: 9)(SEQ ID NO: 960) 81 GPIb beta GGAGTTCGGTCGGGTTTT (SEQ ID NO: 7)(SEQ ID NO: 1005) 82 GPIb beta GGAGTTTGGTTGGGTHT (SEQ ID NO: 7)(SEQ ID NO: 1006) 83 CALCA ATTAGGTTCGTGTTTTAG (SEQ ID NO: 14)(SEQ ID NO: 953) 84 CALCA ATTAGGTTTGTGTTTTAG (SEQ ID NO: 14)(SEQ ID NO: 954) 85 PTGS2 AGTTATTTCGTTATATGG (SEQ ID NO: 52)(SEQ ID NO: 1007) 86 PTGS2 AGTTATTTTGTTATATGG (SEQ ID NO: 52)(SEQ ID NO: 1008) 87 MYOD1 GTGTTAGTCGTTTAGGGT (SEQ ID NO: 8)(SEQ ID NO: 1009) 88 MYOD1 GTGTTAGTTGTTTAGGGT (SEQ ID NO: 8)(SEQ ID NO: 1010) 89 EYA4 AGTGTATGCGTAGAAGGT (SEQ ID NO: 24)(SEQ ID NO: 923) 90 EYA4 AGTGTATGTGTAGAAGGT (SEQ ID NO: 24)(SEQ ID NO: 924) 91 CSPG2 AAAAATTCGCGAGTTTAG (SEQ ID NO: 21)(SEQ ID NO: 945) 92 CSPG2 AAAAATTTGTGAGTTTAG (SEQ ID NO: 21)(SEQ ID NO: 946) 93 PGR TTAAGTGTCGGATTTGTG (SEQ ID NO: 38)(SEQ ID NO: 1011) 94 PGR TTAAGTGTTGGATTTGTG (SEQ ID NO: 38)(SEQ ID NO: 1012) 95 PCNA TAAAGAGGCGGGGAGATT (SEQ ID NO: 58)(SEQ ID NO: 1013) 96 PCNA TAAAGAGGTGGGGAGATT (SEQ ID NO: 58)(SEQ ID NO: 1014) 97 MSH3 AGTATTTTCGTTTGAGGA (SEQ ID NO: 34)(SEQ ID NO: 1015) 98 MSH3 AGTATTTTTGTTTGAGGA (SEQ ID NO: 34)(SEQ ID NO: 1016) 99 WT1 TAGTGAGACGAGGTTTTT (SEQ ID NO: 9)(SEQ ID NO: 1017) 100 WT1 TAGTGAGATGAGGTHTT (SEQ ID NO: 9)(SEQ ID NO: 1018) 101 MYC TTATAATGCGAGGGTTTG (SEQ ID NO: 35)(SEQ ID NO: 1019) 102 MYC TTATAATGTGAGGGTTTG (SEQ ID NO: 35)(SEQ ID NO: 1020) 103 HIC-1 TTTTAGAGCGTTAGGGTT (SEQ ID NO: 27)(SEQ ID NO: 1021) 104 HIC-1 TTTTAGAGTGTTAGGGTT (SEQ ID NO: 27)(SEQ ID NO: 1022) 105 PTGS2 ATATTTGGCGGAAATTTG (SEQ ID NO: 52)(SEQ ID NO: 1023) 106 PTGS2 ATATTTGGTGGAAATTTG (SEQ ID NO: 52)(SEQ ID NO: 1024) 107 EGFR ATTTGGTTCGATTTGGAT (SEQ ID NO: 23)(SEQ ID NO: 931) 108 EGFR ATTTGGTTCGATTTGGAT (SEQ ID NO: 23)(SEQ ID NO: 932) 109 LKB1 TTTAGGTTCGTAAGTTTA (SEQ ID NO: 30)(SEQ ID NO: 965) 110 LKB1 TTTAGGTTTGTAAGTTTA (SEQ ID NO: 30)(SEQ ID NO: 966) 111 IGF2 TTGTATGGTCGAGTTTAT (SEQ ID NO: 29)(SEQ ID NO: 941) 112 IGF2 TTGTATGGTTGAGTTTAT (SEQ ID NO: 29)(SEQ ID NO: 942) 113 PTEN AGAGTTATCGTTTTGTTT (SEQ ID NO: 39)(SEQ ID NO: 957) 114 PTEN AGAGTTATTGTTTTGTTT (SEQ ID NO: 39)(SEQ ID NO: 958) 115 BCL2 TTTTGTTACGGTGGTGGA (SEQ ID NO: 13)(SEQ ID NO: 1025) 116 BCL2 TTTTGTTATGGTGGTGGA (SEQ ID NO: 13)(SEQ ID NO: 1026) 117 AR AGAGGTTGCGTTTTAGAG (SEQ ID NO: 5)(SEQ ID NO: 1027) 118 AR AGAGGTTGTGTTTTAGAG (SEQ ID NO: 5)(SEQ ID NO: 1028) 119 CDH1 AGGGTTATCGCGTTTATG (SEQ ID NO: 15)(SEQ ID NO: 983) 120 CDH1 AGGGTTATTGTGTTTATG (SEQ ID NO: 15)(SEQ ID NO: 984)

TABLE 6 Oligonucleotides used in differentiation betweencolon carcinoma tissue and colon adenoma tissue. No: Gene Oligo: 1CDKN2a GTTGTTTTCGGTTGGTGT (SEQ ID NO: 18) (SEQ ID NO: 1029) 2 CDKN2aGTTGTTTTTGGTTGGTGT (SEQ ID NO: 18) (SEQ ID NO: 1030) 3 GPIb betaGGAGTTCGGTCGGGTTTT (SEQ ID NO: 7) (SEQ ID NO: 1005) 4 GPIb betaGGAGTTTGGTTGGGTTTT (SEQ ID NO: 7) (SEQ ID NO: 1006)

TABLE 7 Crossreference table to relate numbers used in figure labellingto ID numbers used throughout the document Number in FIGS. Gene nameHealthy vs Non-Healthy 50-D CDH13 20-C CD44 54-C TPEF (=TMEFF2; =HPP1)21-C CSPG2 50-C CDH13 25-B GSTP1 43-C TGFBR2 36-B N33 49-A CAV1 52-CPTGS2 46-A TP73 54-B TPEF (=TMEFF2; =HPP1) 20-A CD44 24-D EYA4 24-B EYA426-B GTBP/MSH6 4-C EGR4 15-E CDH1 23-E EGFR 30-B LKB1 22-D DAPK1 29-DIGF2 10-A HLA-F 29-C IGF2 36-C N33 21-D CSPG2 39-D PTEN 32-B MLH1 26-AGTBP/MSH6 14-C CALCA 22-C DAPK1 39-C PTEN 9-D WT1 23-A EGFR 21-A CSPG230-A LKB1 9-C WT1 60-E ESR1 12-A APC 29-A IGF2 8-D MYOD1 36-A N33 54-ATPEF (=TMEFF2; =HPP1) 18-E CDKN2a 15-D CDH1 12-C APC Healthy vsCarcinoma 50-D CDH13 54-C TPEF (=TMEFF2; =HPP1) 50-C CDH13 21-C CSPG220-C CD44 24-B EYA4 12-A APC 52-C PTGS2 24-D EYA4 39-B PGR 25-B GSTP149-A CAV1 23-E EGFR 36-B N33 29-C IGF2 10-D HLA-F 54-B TPEF (=TMEFF2;=HPP1) 46-A TP73 Healthy vs Adenoma 20-C CD44 10-A HLA-F 43-C TGFBR226-A GTBP/MSH6 26-B GTBP/MSH6 30-B LKB1 20-A CD44 36-C N33 50-D CDH1346-A TP73 39-D PTEN 36-B N33 54-C TPEF (=TMEFF2; =HPP1) 25-B GSTP1 23-AEGFR 40-A RARB 36-D N33 49-A CAV1 54-B TPEF (=TMEFF2; =HPP1) 18-E CDKN2a36-A N33 32-B MLH1 12-C APC 21-C CSPG2 15-E CDH1 52-C PTGS2 62-D RASSF19-C WT1 18-D CDKN2a 60-E ESR1 29-D IGF2 8-D MYOD1 50-C CDH13 4-C EGR442-C S100A2 22-D DAPK1 31-E MGMT 24-D EYA4 56-A CEA 9-D WT1 7-E GPIbbeta 14-C CALCA 52-D PTGS2 8-B MYOD1 24-B EYA4 21-D CSPG2 38-C PGR 58-APCNA 34-D MSH3 9-B WT1 35-B MYC 27-C HIC-1 52-B PTGS2 23-E EGFR 30-ALKB1 29-C IGF2 39-C PTEN 13-D BCL2 5-B AR 15-D CDH1 Carcinoma vs Adenoma18-B CDKN2a 7-E GPIb beta

What is claimed is:
 1. A method for detecting colorectal cancer or colonadenomas or risk thereof in a human subject, comprising: a) contactinggenomic DNA in a biological sample obtained from the subject comprisingcolorectal DNA, with a reagent or series of reagents comprising at leastone of bisulfite, hydrogen sulfite or disulfite; b) comparing thenucleic acid sequence of untreated genomic DNA as set forth in SEQ IDNO: 54 to corresponding nucleic acid sequence derived from SEQ ID NO: 54by bisulfite treatment according to method step a) based on thedifferential base-pairing properties of uracil and cytosine; c)determining the methylation status of one or more CpG dinucleotideswithin the genomic region defined in method step b) by detectingunconverted cytosine bases in this region; and d) detecting colorectalcancer or colon adenomas or risk thereof in the human subject bycomparing the methylation state of at least one CpG position within thenucleic acid sequence of method step b) to the methylation state of thesame CpG position or positions in genomic DNA derived from a humancontrol subject not suffering from colorectal cancer or colon adenomas,wherein a higher degree of CpG methylation in the sample, compared tothat of the control, indicates a presence or an increased likelihood ofcolorectal cancer or colon adenomas.
 2. The method of claim 1, whereinin method step c) a portion or fragment of the treated DNA derived fromSEQ ID NO: 54 is amplified by means of a polymerase chain reaction (PCR)to provide an amplificate.
 3. The method of claim 2, wherein at least 10different fragments, each fragment having a length of 10 to 200 basepairs, are amplified.
 4. The method of claim 2, wherein theamplification step is carried out using one or more sets of primeroligonucleotides suitable to amplify a nucleic acid sequence selectedfrom the group consisting of SEQ ID NOs: 239, 240, 367 and 368 andamplifiable portions thereof.
 5. The method of claim 2, whereindetermining the methylation status of at least one CpG dinucleotidecomprised by SEQ ID NO: 54 comprises hybridization of the amplificate tooligonucleotides or peptide nucleic acid (PNA) oligomers.
 6. The methodof claim 2, wherein the amplificates are labeled with a fluorescentlabel.
 7. The method of claim 1, wherein the method differentiatesbetween normal colon tissue and a tissue selected from the groupconsisting of colon adenoma tissue and colon carcinoma tissue.